[BioC] issues with xps filter

[cstrato]

Dear Larry,

When using the Test3 examples coming with xps I get the following:

 > scheme.test3 <- root.scheme(paste(.path.package("xps"), 
"schemes/SchemeTest3.root", sep="/"))
 > data.test3 <- root.data(scheme.test3, paste(.path.package("xps"), 
"rootdata/DataTest3_cel.root", sep="/"))
 > data.rma <- rma(data.test3, "Test3RMA", tmpdir="", 
background="pmonly", normalize=TRUE)

 > preflr <- PreFilter(mad = c(0.25))
 > rma.pfr <- prefilter(data.rma, "tmp_prefilter", getwd(), 
filter=preflr, minfilters=1, logbase="log2")
Creating new temporary file 
</Volumes/CoreData/CRAN/schemes/tmp_prefilter.root>...
Opening file 
</Users/rabbitus/Library/R/2.11/library/xps/schemes/SchemeTest3.root> in 
<READ> mode...
Opening file </Volumes/CoreData/CRAN/schemes/Test3RMA.root> in <READ> 
mode...
Prefilter: <41> genes of <345> genes fulfill filter criteria.
Opening file 
</Users/rabbitus/Library/R/2.11/library/xps/schemes/SchemeTest3.root> in 
<READ> mode...
Opening file </Volumes/CoreData/CRAN/schemes/tmp_prefilter.root> in 
<READ> mode...
Opening file </Volumes/CoreData/CRAN/schemes/tmp_prefilter.root> in 
<READ> mode...
Exporting data from tree <PreFilter> to file 
</Volumes/CoreData/CRAN/schemes/tmp_prefilter.txt>...

 > tmp <- validData(rma.pfr)
 > d <- dim(tmp[tmp[, "FLAG"] == 1,])
 > d
[1] 41  2

 > x <- validData(data.rma)
 > x <- log(x)/log(2)
 > mads <- apply(x, 1, mad)
 > sum(mads > 0.25)
[1] 41

As you can see, in both cases I get the same result.

Did you copy/paste the code you have sent?
Could you give the sessionInfo() so that I know which version of xps you 
are using?
Could you please run this example and tell me if your result differs 
from the one above?
Furthermore, which array type are you using?

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


On 6/30/10 7:01 PM, Larry N. Singh wrote:
>
> Hi everyone,
>
> I'm having some issues with the madFilter in xps.  Please see below:
>
> # Please note I've already loaded the RMA data in data.rma
> preflr<- Prefilter(mad = c(0.25))
> rma.pfr<- prefilter(data.rma, "tmp_prefilter", getwd(),
> filter=preflr, minfilters=1, logbase="log2")
>
> tmp<- validData(rma.pfr)
> d<- dim(tmp(tmp[, "FLAG"] == 1,])
>
>> d
> 208 2
>
> #### BUT
>
> x<- validData(data.rma)
> x<- log(x)/log(2)
> mads<- apply(x, 1, mad)
>
>> sum(mads>  0.25)
> [1] 3641
>
> I don't get the same numbers for MAD filtering.
> Can someone please tell me what I'm missing here?
>
> Thank you kindly for any help.
> -Larry.
>
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