[BioC] problem with justGCRMA

[James W. MacDonald]

Hi Brian,

Brian_Hare at vrtx.com wrote:
> Hi All,
> 
> I just noticed that justGCRMA in Bioconductor 2.5  output identical 
> intensities across all samples for a subset of probesets on HGU133plus2 
> chip.  I used the command:
> 
>> data <- justGCRMA()
> 
> I've seen it on a couple datasets - one run on linux, one on a PC.  The 
> dataset run on linux is in GEO (GSE9843).  I haven't looked carefully but 
> it seems to occur for some of the lower-intensity probesets. 
> 
> I wonder is this a bug?

No, but it _is_ documented in the mailing list archives:

http://article.gmane.org/gmane.science.biology.informatics.conductor/5665/match=gcrma

 > suppressMessages(library(gcrma)
 > eset <- justGCRMA()
Computing affinitiesLoading required package: AnnotationDbi
.Done.
Adjusting for optical effect.............Done.
Adjusting for non-specific binding............Done.
Normalizing
Calculating Expression
 > a <- apply(exprs(eset), 1, var)
 > sum(a == 0)
[1] 693

 > eset2 <- justGCRMA(fast=F)
Computing affinities.Done.
Adjusting for optical effect.............Done.
Adjusting for non-specific binding............Done.
Normalizing
Calculating Expression
 > b <- apply(exprs(eset2),1,var)
 > sum(b == 0)
[1] 0

Best,

Jim


 >
> 
> Thanks,
> 
> Brian
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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