[BioC] Different RMA expression values in different BioC versions?

[Quanli Wang]

Thank you all for the quick responses. Now seems that I figured out the 
problem. It has nothing todo with BioC but seems to me that it has 
something to do with the different implementations of "merge" function in 
R2.3.1 and R2.4.0. When I tried to reorder the expression values using 
merge function from R based on one prefered probeid list with "sort" 
option set to FALSE,R2.3.1 gives an order based on the x, while R2.4.0 
gives an order based on y.

Here is the little legacy script that does the ordering:

eset <- read.table("eset.RData")
geneID <- geneNames(eset)
genedescriptorfile = "C:\\CAGP\\9999\\cel\\h133+.genedescriptors"
genedes <- read.table(genedescriptorfile,sep="\t",header=FALSE, row.names=NULL)
rmamatrix2 <- cbind(geneID,rmamatrix)
cprmamatrix <-
merge(x=rmamatrix2,y=genedes,by.x=1,by.y=1,all.x=FALSE,all.y=FALSE,sort=FALSE)
rmamatrix <- cprmamatrix[,2:ncol(rmamatrix2)]

Can someone verify that it is indeed the case even it is more like an R 
problem, not a BioC problem.

Best, Quanli


   On 
Wed, 10 Jan 2007, James W. MacDonald wrote:

> Quanli Wang wrote:
>>> Different than what? An earlier version with the same chips?
>> 
>> Yes. For the same chips using justRMA, the values from R2.3.1/BioC1.8 will 
>> be very different from that from R2.4.0/BioC1.9.
>> Quanli
>
> I don't see that here. I get identical results for the same chips using these 
> two versions of R/BioC
>
>> eset <- justRMA()
> Background correcting
> Normalizing
> Calculating Expression
>> save(eset, file="eset2.3.1.Rdata")
>> sessionInfo()
> Version 2.3.1 (2006-06-01)
> i386-pc-mingw32
>
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
> "datasets"
> [8] "base"
>
> other attached packages:
> hgu133plus2cdf           affy         affyio        Biobase
>      "1.12.0"       "1.10.0"        "1.0.0"       "1.10.1"
>
> [close R-2.3.1, start R-2.4.0]
>
>> eset2 <- justRMA()
> Background correcting
> Normalizing
> Calculating Expression
>> load("eset2.3.1.Rdata")
>> all.equal(exprs(eset), exprs(eset2))
> [1] TRUE
>> sessionInfo()
> R version 2.4.1 (2006-12-18)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils" "datasets" 
> "methods"
> [8] "base"
>
> other attached packages:
> hgu133plus2cdf           affy         affyio        Biobase
>      "1.14.0"       "1.12.2"        "1.2.0"       "1.12.2"
>
> Can you show the code you used to get different results, and the output of 
> sessionInfo(), as requested in my last email?
>
> Best,
>
> Jim
>
>
>> 
>> _______________________________________________
>> 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
>
>
>