[BioC] Agilent zebrafish4x44 database
Neel Aluru
naluru at whoi.edu
Fri Nov 13 04:35:39 CET 2009
Thanks, Francois. I am a beginner to R and slowly trying to learn. I appreciate your comments. Now I have pasted the session info. You may be right with regard to ACCNUM mapping. I looked in the zebrafish.db0 package and cannot find the ACCNUMmapping. I do not understand what you meant by space in "zebrafish.db0".
Thanks once again,
Sincerely, Neel
Following is the session info.
R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
> getwd()
[1] "/Users/Neel"
> setwd("/Users/Neel/agilent")
> getwd()
[1] "/Users/Neel/agilent"
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: limma
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: genefilter
Loading required package: affyPLM
Loading required package: affy
Attaching package: 'affy'
The following object(s) are masked from package:Agi4x44PreProcess :
plotDensity
Loading required package: gcrma
Loading required package: Biostrings
Loading required package: IRanges
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
Loading required package: preprocessCore
Attaching package: 'affyPLM'
The following object(s) are masked from package:Agi4x44PreProcess :
RLE
The following object(s) are masked from package:stats :
resid,
residuals,
weights
Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
there is no package called 'beadarray'
Error: package/namespace load failed for 'arrayQualityMetrics'
Loading required package: tcltk
Loading Tcl/Tk interface ... done
limmaGUI can be launched by typing limmaGUI()
Attaching package: 'limmaGUI'
The following object(s) are masked from package:limma :
limmaUsersGuide
limmaGUI can be launched by typing limmaGUI()
Attaching package: 'limmaGUI'
The following object(s) are masked from package:limma :
limmaUsersGuide
> library("Agi4x44PreProcess")
> targets=read.targets(infile="infile.txt")
Target File
X FileName Treatment GErep
conta cont1 conta.txt control 1
contb cont2 contb.txt control 2
contc cont3 contc.txt control 3
contd cont4 contd.txt control 4
pcba pcb1 pcba.txt pcb 1
pcbb pcb2 pcbb.txt pcb 2
pcbc pcb3 pcbc.txt pcb 3
pcbd pcb4 pcbd.txt pcb 4
> aa=read.AgilentFE(targets, makePLOT=TRUE)
Read conta.txt
Read contb.txt
Read contc.txt
Read contd.txt
Read pcba.txt
Read pcbb.txt
Read pcbc.txt
Read pcbd.txt
RGList:
dd$R: 'gProcessedSignal'
dd$G: 'gMeanSignal'
dd$Rb: 'gBGMedianSignal'
dd$Gb: 'gBGUsed'
> CV.rep.probes(aa, "zebrafish.db", foreground="MeanSignal", raw.data= TRUE, writeR=FALSE,targets)
------------------------------------------------------
Non-CTRL Replicated probes
foreground: MeanSignal
FILTERING BY ControlType FLAG
RAW DATA: PROBES AFTER ControlType FILTERING: 42990
Error: getAnnMap: zebrafish.db package not attached and load is FALSE
Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) :
error in evaluating the argument 'envir' in selecting a method for function 'mget'
> aaNORM = BGandNorm(aa, BGmethod = "half", NORMmethod = "quantile", foreground = "MeanSignal", background = "BGMedianSignal", offset = 50, makePLOTpre = TRUE, makePLOTpost = TRUE)
BACKGROUND CORRECTION AND NORMALIZATION
foreground: MeanSignal
background: BGMedianSignal
Hit <Return> to see next plot:
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BGmethod: half
NORMmethod: quantile
OUTPUT in log-2 scale
------------------------------------------------------
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End of the session
On Nov 12, 2009, at 9:36 PM, Francois Pepin wrote:
> Hi Neel,
>
> in cases like this, supplying the sessionInfo() is a good idea, as it lets everyone know which versions you are using. As per the posting guide (see the URL at the bottom of this e-mail), having the code snippet initially would also have been helpful.
>
> I don't have the zebrafish.db0 package installed, so I can't say for sure what the issue is. I don't think you should have the space in "zebrafish.db0 ". It might also be that the zebrafish.db0 package does not have the ACCNUM mapping.
>
> Now that we've got more information, the others can chime in with more insight.
>
> Francois
>
> On 11/12/2009 09:08 PM, Neel Aluru wrote:
>> Hi Francois,
>>
>> Thanks for your reply. I am trying to calculate the replicated probe coefficient of variation and having trouble understanding it. Here is the syntax I am writing for it.
>>
>>> CV.rep.probes(aa,"zebrafish.db0 ",foreground ="MeanSignal", raw.data=TRUE, writeR = TRUE, targets)
>> The error message is
>>
>> Non-CTRL Replicated probes
>> foreground: MeanSignal
>> FILTERING BY ControlType FLAG
>> RAW DATA: PROBES AFTER ControlType FILTERING: 42990
>>
>> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
>> object 'zebrafish.db0ACCNUM' not found
>> Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) :
>> error in evaluating the argument 'envir' in selecting a method for function 'mget'
>>
>> I defined "aa" for reading agilent FE files.
>>
>> I am not sure if I am doing something wrong. I really appreciate any suggestions how to proceed with it.
>>
>> Thanks,
>>
>> Sincerely, Neel
>>
>> On Nov 12, 2009, at 3:31 PM, Francois Pepin wrote:
>>
>>> Hi Neel.
>>>
>>> I'm not sure which database you are talking about here.
>>>
>>> I haven't used zebrafish arrays, but my experience with human and mouse is that there is very little variation between duplicated probes (ie same sequence and probe id). I would be surprised if zebrafish is any different, as those differences would be purely technical and only depend on the protocol, the reagents used and the person performing the manipulations.
>>>
>>> Maybe you could clarify if I'm not reading this properly, as I'm confused what a database would have to do with this.
>>>
>>> Francois
>>>
>>> On 11/12/2009 03:19 PM, Neel Aluru wrote:
>>>> Hello,
>>>>
>>>> Does any one has Agilent zebrafish 4x44 database to use for calculating % CV of replicated probes.
>>>>
>>>> Thank you,
>>>>
>>>> Neel
>>>>
>>>>
>>>> Neel Aluru
>>>> Postdoctoral Scholar
>>>> Biology Department
>>>> Woods Hole Oceanographic Institution
>>>> Woods Hole, MA 02543
>>>> USA
>>>> 508-289-3607
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> Neel Aluru
>> Postdoctoral Scholar
>> Biology Department
>> Woods Hole Oceanographic Institution
>> Woods Hole, MA 02543
>> USA
>> 508-289-3607
>>
>>
>>
>
Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607
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