[BioC] Final: Masking single Oligos in mas5
Benjamin Otto
b.otto at uke.uni-hamburg.de
Wed Dec 28 11:12:50 CET 2005
Hi Ariel, hi folks,
I finally managed the problems discussed in the thread here so I would like
to add some final notes. In the case of saving the environment I forgot to
put the new cdf environment name in quotas:
wrong:
------
$> newcdf <- wrapCdfEnvAffy(hgu133plus2cdf,1164,1164,"hgu133plus2cdf")
$> envnewcdf <- as(newcdf,"environment")
$> # here comes the error
$> x at cdfName <- envnewcdf
correct:
--------
$> newcdf <- wrapCdfEnvAffy(hgu133plus2cdf,1164,1164,"hgu133plus2cdf")
$> envnewcdf <- as(newcdf,"environment")
$> x at cdfName <- "envnewcdf"
The second problem was the painful removing of certain probes and probesets.
The main trigger for a lot of problems in my case turned out to be the grep
command in the RemoveProbes() function (in line 24, where line 1 is the
function header):
$ ii <-grep(paste("^",pset[i],sep=""),probes[,1])
Thats because I'm using the "hgu133plus2" cdf package which contains a huge
amount of geneNames AND especially very similar names like:
$[1] "121_at" "1563121_at" "217121_at" "218121_at" "227121_at" "233121_at"
In this case here the command above returns:
$[1] 1 2 3 4 5 6 7 8 9 10 11 12
13 14 5894 5895 5896 5897 5898 5899 5900 5901 5902 35353 35354
$[26] 35355 35356 35357 35358 35359 35360 35361 37097 37098 37099 37100
37101 37102 37103 37104 37105 49109 49110 49111 49112 49113 49114 49115
53540 53541
$[51] 53542 53543 53544 53545 53546 53547 53548
while it should only return:
$[1] 1 2 3 4 5 6 7 8 9 10 11 12
13 14
This had two major effects in my case:
1. A lot more probes are deleted than desired.
2. The function needed nearly 6-7 hours to finish calculation in stead of a
few minutes.
Summary:
--------
A)
I would propose substituting the grep command in RemoveProbes() with the
more sensitive version:
$ ii <-grep(paste("^",pset[i],sep=""),probes[,1])
which now works fine for me.
B)
The command sequence for storing the environment afterwards seems to follow
the vignette of Laurent Gautier and would be:
$> newcdf <- wrapCdfEnvAffy(hgu133plus2cdf,1164,1164,"hgu133plus2cdf")
$> envnewcdf <- as(newcdf,"environment")
$> x at cdfName <- "envnewcdf"
$> save(x,newcdf,envnewcdf,file="/home/otto/R/createdEnvTest.env")
Finally, thanky very much Ariel for your help AND the definitely very
helpful functions!!! Now that every thing works fine in my case too I am
really enthusiastic over the speed the new environments get calculated with.
:-)
Regards,
Benjamin
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Benjamin
> Otto
> Sent: 15 December 2005 13:32
> To: Ariel Chernomoretz; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] [SPAM???] Re: Masking single Oligos in mas5
>
>
> Hi Ariel,
>
> I have been experimenting with the new function "RemoveProbes2"
> unfortunately without success. However that might be due to the fact that
> I'm not sure how to save the environment. For the saving steps I followed
> the vignette of Laurent Gautier under
> "www.bioconductor.org/repository/devel/vignette/ngenomeschips.pdf".
> To be precise I used the following commands
>
> > cdfpackagename
> [1] "hgu133plus2cdf"
> > probepackagename
> [1] "hgu133plus2probe"
> > plcdf <- wrapCdfEnvAffy(hgu133plus2cdf,1164,1164,"hgu133plus2cdf")
> > envplcdf <- as(plcdf,"environment")
> > x at cdfName <- envplcdf
> > save(x,plcdf,envplcdf,file="HGU133P2x200.rda")
> >
>
> which seemed to work fine, but I can't tell for sure. Now when I
> called the
> new function it pretends the file doesn't contain any cdf information !?
>
> > cdfpackagename
> [1] "hgu133plus2cdf"
> > probepackagename
> [1] "hgu133plus2probe"
> >
> RestoreCdfEnv(clean.cdf="HGU133P2x200.rda",cdfpackagename,probepac
> kagename)
> Warning: package 'hgu133plus2cdf' is in use and will not be installed
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered:
> Specified environment does not contain hgu133plus2
> HGU133P2x200.rda
> Data for package affy did not contain hgu133plus2cdf
> HGU133P2x200.rda
>
> I'm aware that most probably the environment doesn't get stored
> correctly in
> the file at the first place. Yet, I didn't find any convinient alternative
> for doing so.
>
> Regards,
> Benjamin
>
> P.S.: And a merry 1st, 2nd and 3rd Advent
>
>
>
>
> > -----Original Message-----
> > From: bioconductor-bounces at stat.math.ethz.ch
> > [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Ariel
> > Chernomoretz
> > Sent: 06 December 2005 19:55
> > To: bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] [SPAM???] Re: Masking single Oligos in mas5
> >
> >
> > Hi Benjamin
> >
> > mmm...try replacing
> > the line :
> >
> > $ tmp <- as.vector(ans[[i]][, i.probes])
> >
> > with
> >
> > $ tmp <- as.vector(as.matrix(ans[[i]])[, i.probes])
> >
> >
> >
> >
> > here is why i think that may work...
> >
> > > l<-list(1,as.matrix(1))
> > > l[[1]][,1]
> > Error in l[[1]][, 1] : incorrect number of dimensions
> > > l[[2]][,1]
> > [1] 1
> > > as.matrix(l[[1]])[,1]
> > [1] 1
> >
> >
> > regards
> > ariel./
> >
> >
> >
> > On December 6, 2005 12:54 pm, Benjamin Otto wrote:
> > > Hi Ariel,
> > >
> > > well I wish you a loooot of luck then for the pre-postdoc time.
> > I hope you
> > > like your new job. :-)
> > >
> > > I think I have localized the problem for the function crash although I
> > > don't quite understand it yet. I was just writing this text when your
> > > answer reached me. Thanks!
> > > Back to the crash: I will just give two examples for better
> explanation.
> > >
> > > #Example 1: Include all probes of the probeset 117_at
> > > # with exception of the first probe
> > > # and don't delete the set itself
> > > $> listOutProbes <- c("117_at2","117_at3","117_at4",
> > > $+ "117_at5","117_at6","117_at7","117_at8","117_at9",
> > > $+ "117_at10","117_at11","117_at12","117_at13",
> > > $+ "117_at14","117_at15","117_at16")
> > >
> > > $> sets <- NULL
> > > $> ResetEnvir(cdfpackagename,probepackagename)
> > > $> RemoveProbes(probes,sets,cdfpackagename,probepackagename)
> > >
> > >
> > > #Example 2: Exapmle 1 again but ...
> > > # ... delete the set from the list
> > > $> listOutProbes <- c("117_at2","117_at3","117_at4",
> > > $+ "117_at5","117_at6","117_at7","117_at8","117_at9",
> > > $+ "117_at10","117_at11","117_at12","117_at13",
> > > $+ "117_at14","117_at15","117_at16")
> > >
> > > $> sets <- ("117_at")
> > > $> ..
> > > $> ..
> > >
> > >
> > > ONLY the construction in example number 1!!! returns the
> error message:
> > >
> > > $ Error in ans[[i]][, i.probes] : incorrect number of dimensions
> > >
> > > and that when it reaches the command:
> > >
> > > $ pmIndex <- unlist(indexProbes(newAB,"pm"))
> > >
> > > in function "RemoveProbes". Note that the command
> > "indexProbes(newAB,"pm")"
> > > is causing the problem. That's why I snooped into the code of
> the method
> > > "indexProbes" and voila ... the problem source is finally the command:
> > >
> > > $ tmp <- as.vector(ans[[i]][, i.probes])
> > >
> > > where "ans" was created by
> > >
> > > $> envir <- getCdfInfo(newAB)
> > > $> genenames <- ls(envir)
> > > $> ans <- mget(genenames, envir, ifnotfound = NA)
> > >
> > >
> > > NOW: If ans[[i]] contains only ONE value for each of "pm" and
> "mm" then
> > >
> > > $> ans[[i]][,"pm"],
> > > $> ans[[i]][,"mm"]
> > > or ...
> > > $> ans[[i]][,c(1,2)]
> > >
> > > causes R to return the error message. I don't know whether
> the following
> > > observation has to do with that or is rather neglectable:
> > >
> > > $ # for the probeset with only one probe left I get:
> > > $ Browse[1]> ans[[i]][1]
> > > $ pm
> > > $1051223
> > >
> > > $ # for a probeset with more probes left I get:
> > > $ Browse[1]> ans[[i]][1]
> > > $ [1] 1051223
> > >
> > >
> > > FINALLY: Sounds as if the bells should ring in ecstasy in my
> > head telling
> > > me what the problem really is, unfortunately I don't
> understand it yet.
> > > Maybe someone has an idea whether this is some kind of
> expected problem
> > > which could be corrected by the way "ans" is created. I think I
> > will have
> > > to experiment a little bit more...
> > >
> > > regards,
> > > Benjamin
> > >
> > > > -----Original Message-----
> > > > From: bioconductor-bounces at stat.math.ethz.ch
> > > > [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Ariel
> > > > Chernomoretz
> > > > Sent: 06 December 2005 17:10
> > > > To: bioconductor at stat.math.ethz.ch
> > > > Subject: Re: [BioC] [SPAM???] Re: Masking single Oligos in mas5
> > > >
> > > >
> > > >
> > > >
> > > > Hi Benjamin
> > > >
> > > > I am sorry you have problems with the code.
> > > >
> > > > Regarding the computation time, yes. It is slow even with
> > small/mid sized
> > > > lists, so in your case I would expect a loooot of processing time
> > > > (more RAM
> > > > would help also ;-) ). I guess that to improve this, the
> > > > function should be
> > > > completely rewritten using perhaps a different approach.
> > > >
> > > > However, once you succed in generating a modified cdf
> > > > environment, and if you
> > > > are planning to compute expressions many times having the
> same probes
> > > > removed, you should keep (save) the modified cdf environment as
> > > > an R object.
> > > > I wrote a function (RemoveProbes2, included at the end)
> that takes the
> > > > clean.cdf.environment as an input argument. So everything should
> > > > be faster
> > > > for subsequent calculations.
> > > >
> > > >
> > > > Unfortunately I am not a lot at the office these days. My postdoc
> > > > is about to
> > > > end here, and I am moving in a couple of weeks, so things are a
> > > > little bit
> > > > caotic this days! However I will check your code asap.
> > > >
> > > > quick observations/questions:
> > > > 1) are you removing entire probesets specifiyng the whole set of
> > > > probes via
> > > > the rmd$Probes list AND the rmd$Set?
> > > > 2) if you plan to use presence calls, be cautious. After the
> > > > probe removal
> > > > step you end up with probeset with different number of probes so
> > > > be carefull
> > > > with the significance levels of the Wilcoxon'rank test
> > > >
> > > >
> > > >
> > > > Regards,
> > > > Ariel./
> > > >
> > > >
> > > >
> > > >
> > > > ################################################
> > > > # clean.cdf: a modified cdf environment. Should be generated
> > > > # using RemoveProbes and saving the modified
> > > > # environment afterwards
> > > > # cdfpackagename: (e.g. "hgu95av2cdf")
> > > > # probepackagename: (e.g. "hgu95av2probe")
> > > > # destructive: unimplemented option, see NOTE
> > > > RemoveProbes2<-function(clean.cdfenv =NULL,
> > > >
> > > > cdfpackagename,probepackagename,destructive=TRUE){
> > > >
> > > > #default probe dataset values
> > > > probe.env.orig <- get(probepackagename)
> > > >
> > > >
> > > >
> > > > if(is.null(clean.cdfenv)){
> > > > cat("A cdfenv should be provided\n")\
> > > > return();
> > > > }else{ #clean.cdf provided. much, much faster!
> > > > ipos<-grep(cdfpackagename,search())
> > > > rm(list=c(cdfpackagename),pos=ipos)
> > > > assign(cdfpackagename,clean.cdfenv,pos=ipos)
> > > > }
> > > >
> > > >
> > > > # setting the PROBE env accordingly (idea from gcrma
> > > > compute.affinities.R)
> > > > tmp <- get("xy2i",paste("package:",cdfpackagename,sep=""))
> > > > newAB <- new("AffyBatch",cdfName=cleancdf)
> > > > pmIndex <- unlist(indexProbes(newAB,"pm"))
> > > > subIndex<- match(tmp(probe.env.orig$x,probe.env.orig$y),pmIndex)
> > > > rm(newAB)
> > > > iNA <- which(is.na(subIndex))
> > > >
> > > > if(length(iNA)>0){
> > > > ipos<-grep(probepackagename,search())
> > > > assign(probepackagename,probe.env.orig[-iNA,],pos=ipos)
> > > > }
> > > > }
> > > >
> > > > ###############################################
> > > >
> > > > On December 6, 2005 04:07 am, Benjamin Otto wrote:
> > > > > Hi folks,
> > > > >
> > > > > sorry for taking your time again. I let the computer finish the
> > > > > "removeProbes"-calculation over night, so I don't know how long he
> > > > > took...to finally display the following error message:
> > > > >
> > > > > "Error in ans[[i]][, i.probes] : incorrect number of dimensions"
> > > > >
> > > > > You can imagine how desperately I was looking for a shotgun
> > > >
> > > > that moment. To
> > > >
> > > > > provide maybe more information I forgot to submit in my
> last thread
> > > > > here come the commands and extracts of my lists /
> structures I used:
> > > > >
> > > > > $# libraries used
> > > > > $> library(simpleaffy)
> > > > > $> library(affydata)
> > > > > $> require(gcrma)
> > > > > $
> > > > > $# preliminary commands
> > > > > $> setwd ("....")
> > > > > $> x <- read.affy()
> > > > > $> x at cdfName <- "HGU133Plus2"
> > > > > $> cleancdf <- cleancdfname(x at cdfName,addcdf=FALSE)
> > > > > $> cdfpackagename <- paste(cleancdf,"cdf",sep="")
> > > > > $> probepackagename <- paste(cleancdf,"probe",sep="")
> > > > > $> ResetEnvir(cdfpackagename,probepackagename)
> > > > > $
> > > > > $# my function for indentification of unwanted oligos
> > > > > $# I will append the function code below
> > > > > $> rmd <- get.foul.oligos(x, ratio=2, diff=100)
> > > > > $
> > > > > $# the initial rma/mas calculation without changes
> > > > > $> d.rma <- rma(x)
> > > > > $> d.gcrma <- gcrma(x)
> > > > > $> d.mas <- mas5(x)
> > > > > $> d.mas.call <- mas5calls(x)
> > > > > $
> > > > > $# The command for invoking the removeProbes function
> > > > > $>
> RemoveProbes(rmd$Probes,rmd$Set,cdfpackagename,probepackagename)
> > > > >
> > > > >
> > > > > The probe list "rmd$Probes" contains 565825 entries, the set
> > > >
> > > > list "rmd$Set"
> > > >
> > > > > 32791 entries. A little structure check:
> > > > >
> > > > > $> rmd$Set[1:5]
> > > > > $[1] "1007_s_at" "1053_at" "1255_g_at" "1405_i_at" "1438_at"
> > > > > $> rmd$Probes[1:5]
> > > > > $[1] "1007_s_at1" "1007_s_at2" "1007_s_at3" "1007_s_at4"
> > "1007_s_at5"
> > > > >
> > > > > Looks fine to me, but is it? What could cause the error
> > message here ?
> > > > >
> > > > > Here comes the code of my function:
> > > > >
> > > > >
> > > > > get.foul.oligos <- function(x,ratio=1,diff=150,verbose=FALSE) {
> > > > >
> > > > > remove <- list()
> > > > > remove$Probes <- list()
> > > > > remove$Set <- list()
> > > > > len.plist <- 0
> > > > > len.slist <- 0
> > > > >
> > > > >
> > > > > ids <- geneNames(x)
> > > > > num.ids <- length(ids)
> > > > > num.samples <- length(pm(x)[1,])
> > > > > msk.table <- matrix(NA,num.ids,2)
> > > > > rm.string <- NA
> > > > >
> > > > > for (i in 1:num.ids) {
> > > > > id <- ids[i]
> > > > > oligos.pm <- indexProbes(x, which="pm",
> > genenames=id)[[id]]
> > > > > oligos.mm <- indexProbes(x, which="mm",
> > genenames=id)[[id]]
> > > > > num.oligos <- length(oligos.pm)
> > > > > num.rm <- 0
> > > > > for (j in 1:num.oligos) {
> > > > > cat ("i:",i," j:",j,"\n")
> > > > > rm.flag <- TRUE
> > > > > for (k in 1:num.samples) {
> > > > > val.pm <-
> > intensity(x)[oligos.pm[j],k]
> > > > > val.mm <-
> > intensity(x)[oligos.mm[j],k]
> > > > > if (val.pm/val.mm > ratio &
> > > >
> > > > val.pm-val.mm > diff) {
> > > >
> > > > > rm.flag <- FALSE
> > > > > }
> > > > > }
> > > > > if (rm.flag == TRUE) {
> > > > > num.rm <- num.rm + 1
> > > > > oligo.name <- paste(id,j,sep="")
> > > > > if (len.plist == 1) {
> > > > > remove$Probes <-
> > > >
> > > > c(remove$Probes,oligo.name)
> > > >
> > > > > }
> > > > > else { remove$Probes <-
> > c(oligo.name) }
> > > > > len.plist <- 1
> > > > >
> > > > > if (is.na(rm.string)) {
> > rm.string <- j }
> > > > > else { rm.string <-
> > > >
> > > > paste(rm.string,j,sep=",") }
> > > >
> > > > > }
> > > > > }
> > > > > if (num.rm == num.oligos) {
> > > > > if (len.slist == 1) {
> > > > > remove$Set <- c(remove$Set,id)
> > > > > }
> > > > > else { remove$Set <- c(id) }
> > > > > len.slist <- 1
> > > > >
> > > > > rm.string <- "all"
> > > > > }
> > > > > }
> > > > > return(remove)
> > > > > }
> > > > >
> > > > > > -----Original Message-----
> > > > > > From: bioconductor-bounces at stat.math.ethz.ch
> > > > > > [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf
> > Of Benjamin
> > > > > > Otto
> > > > > > Sent: 05 December 2005 17:14
> > > > > > To: bioconductor at stat.math.ethz.ch
> > > > > > Subject: Re: [BioC] Masking single Oligos in mas5
> > > > > >
> > > > > >
> > > > > > Hi Ariel and Jenny,
> > > > > >
> > > > > > thanks very much for the quick reply!!! I have been
> experimenting
> > > > > > since with
> > > > > > the functions and it really seems to be what I'm looking
> > for. A small
> > > > > > test with your test_script Ariel returned what I hoped
> > for. However
> > > > > > there is one
> > > > > > aspect confusing me. After writing a little function myself,
> > > > > > which computes
> > > > > > the probe and probeset list which should be excluded in my
> > > >
> > > > case I applied
> > > >
> > > > > > the removeProbes function on these lists. While I'm writing this
> > > > > > message my
> > > > > > computer is still calculating and he has started four
> > hours ago! Is
> > > > > > it normal for the function to be so time consuming or is
> > there some
> > > > > > chance that
> > > > > > I just have done something wrong? I suppose the problem is on my
> > > > > > side but I
> > > > > > just can't imagine what it could be because I followed the
> > > >
> > > > "testscript"
> > > >
> > > > > > steps. But as the reading of the CEL files usually needs just a
> > > > > > few minutes
> > > > > > (maybe five if time consuming) I wouldn't have thought
> > the removing
> > > > > > of probesets would take as long as it currently does. I
> > must confess
> > > > > > my lists are really long. Still the problem is of big importance
> > > >
> > > > for me and
> > > >
> > > > > > so it would be great to get an idea of your experience with
> > > >
> > > > the function
> > > >
> > > > > > perfomance on your systems. Here is a little summary of the
> > > > > > conditions in my
> > > > > > case:
> > > > > >
> > > > > > Chiptype: HG_U133_Plus2
> > > > > > num. samples: 2
> > > > > > num. Probes in listOutProbes: ~ 500.000
> > > > > > num. Sets in listOutProbeSets: ~ 30.000
> > > > > > System: P4 - 3 GHZ, 500 MB RAM,
> > > > > > R-version: RGUI 2.2.0 under WindowsXP.
> > > > > >
> > > > > > Mainly I have been wondering that the removing of
> probes from the
> > > > > > structure
> > > > > > takes so much longer than reading in the CEL files and
> > building the
> > > > > > structure. Has anyone of you maybe started a test before
> > > >
> > > > trying to remove
> > > >
> > > > > > all probesets from an environment? Or can you at least judge
> > > >
> > > > wether the
> > > >
> > > > > > current running time in my case is ok or looks suspicious?
> > > > > >
> > > > > > In any case just to make it clear again, thanks very much in any
> > > > > > case. The functions really seem to be of very, very much
> > help!!! :-)
> > > > > >
> > > > > > Sincerly,
> > > > > > Benjamin
> > > > > >
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: bioconductor-bounces at stat.math.ethz.ch
> > > > > > [mailto:bioconductor-bounces at stat.math.ethz.ch]On
> Behalf Of Ariel
> > > > > > Chernomoretz
> > > > > > Sent: 01 December 2005 17:32
> > > > > > To: bioconductor at stat.math.ethz.ch
> > > > > > Subject: Re: [BioC] Masking single Oligos in mas5
> > > > > >
> > > > > >
> > > > > > Hi Benjamin,
> > > > > >
> > > > > > Some time ago I wrote a couple of functions that modified
> > > > > > the cdf environments in order to remove bad probes from the
> > > >
> > > > affy analysis
> > > >
> > > > > > You could check:
> > > > > >
> > > > > > http://files.protsuggest.org/biocond/html/7350.html
> > > > > > http://files.protsuggest.org/biocond/html/7366.html
> > > > > > http://files.protsuggest.org/biocond/html/7367.html
> > > > > >
> > > > > >
> > > > > > hope that helps.
> > > > > >
> > > > > > ariel./
> > > > > >
> > > > > > On December 1, 2005 11:06 am, Benjamin Otto wrote:
> > > > > > > Hi,
> > > > > > >
> > > > > > > I have been searching for nearly two days for a
> solution to the
> > > > > >
> > > > > > following
> > > > > >
> > > > > > > problem without finding satisfactory answers:
> > > > > > >
> > > > > > > I am working on the analysis of a HG-U133_Plus2 Chip.
> Can I mask
> > > > > > > for certain probesets single Oligos such that the
> > expression, p and
> > > > > > > fold
> > > > > >
> > > > > > change
> > > > > >
> > > > > > > values are calculated based on the remaining oligos?
> > > > > > >
> > > > > > > A better description of my problem and the background. We
> > > >
> > > > are handling
> > > >
> > > > > > > a cross-species experiment having hybradized rna from
> > tupaia on the
> > > > > > > human chip. This resulted in fairly low expression signals.
> > > >
> > > > If we just
> > > >
> > > > > > > forget about all the other putative problems in analysing
> > > >
> > > > the result I
> > > >
> > > > > > > think it seems reasonable to say, that in many cases only
> > > >
> > > > some of the
> > > >
> > > > > > > probeset oligos will have hybridized satisfyingly. So
> > the idea is
> > > > > > > masking some of the oligos by some criteria and calculate
> > > >
> > > > the results
> > > >
> > > > > > > only based upon subsets of the probesets. The problem is:
> > > >
> > > > If I set even
> > > >
> > > > > > > only one single oligo to NA, the values calculated for the
> > > > > > > corresponding
> > > > > >
> > > > > > probeset won't be
> > > > > >
> > > > > > > calculated but set to NA. Most of the threads I found
> concerning
> > > > > > > the masking problem handle the question of an autpmated or
> > > >
> > > > corrected form
> > > >
> > > > > > > of masking. But there seems to be no available
> information about
> > > > > > > our case.
> > > > > >
> > > > > > Has
> > > > > >
> > > > > > > anyone done something like that before? I'm sure there will
> > > >
> > > > have to be
> > > >
> > > > > > some
> > > > > >
> > > > > > > manual programing. But the major question is: Does
> anybody see a
> > > > > > > possibility to mask the single oligos on a top level
> like fixing
> > > > > > > the affybatch structure? Or do I have to change every single
> > > > > >
> > > > > > function to treat
> > > > > >
> > > > > > > NA values in the correct form?
> > > > > > >
> > > > > > > thanks for your help,
> > > > > > > Benjamin
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > Bioconductor mailing list
> > > > > > > Bioconductor at stat.math.ethz.ch
> > > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > > > >
> > > > > > --
> > > > > > Ariel Chernomoretz, Ph.D.
> > > > > > Centre de recherche du CHUL
> > > > > > 2705 Blv Laurier, bloc T-367
> > > > > > Sainte-Foy, Qc
> > > > > > G1V 4G2
> > > > > > (418)-525-4444 ext 46339
> > > > > >
> > > > > > _______________________________________________
> > > > > > Bioconductor mailing list
> > > > > > Bioconductor at stat.math.ethz.ch
> > > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > > > >
> > > > > > _______________________________________________
> > > > > > Bioconductor mailing list
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> > > > >
> > > > > _______________________________________________
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> > > > > Bioconductor at stat.math.ethz.ch
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> > > >
> > > > --
> > > > Ariel Chernomoretz, Ph.D.
> > > > Centre de recherche du CHUL
> > > > 2705 Blv Laurier, bloc T-367
> > > > Sainte-Foy, Qc
> > > > G1V 4G2
> > > > (418)-525-4444 ext 46339
> > > >
> > > > _______________________________________________
> > > > Bioconductor mailing list
> > > > Bioconductor at stat.math.ethz.ch
> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> > --
> > Ariel Chernomoretz, Ph.D.
> > Centre de recherche du CHUL
> > 2705 Blv Laurier, bloc T-367
> > Sainte-Foy, Qc
> > G1V 4G2
> > (418)-525-4444 ext 46339
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>
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