[BioC] issues with xps filter

[cstrato]

Dear Larry,

As already mentioned, when using exon arrays I can reproduce your 
observation. It turns out that for exon arrays I can no longer loop over 
internal unitIDs, which I had changed correctly for the UniFilter code 
but forgot to change for the PreFilter code. Thank you for reporting 
this problem.

I have already uploaded the new version xps_1.8.2 to BioC which should 
be available tomorrow.

I must ask users of xps, who are using function "prefilter()" with exon 
arrays, to upgrade to the new version xps_1.8.2 in order to avoid 
loosing transcripts/probesets satisfying the prefilter conditions (As 
mentioned above function "unifilter()" is not affected). I apologize for 
the inconvenience.

Best regards
Christian


On 6/30/10 10:46 PM, cstrato wrote:
> 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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>
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