



Dear Bioconductor List,


I have repeated my workflow using the affy and oligo package alternatively followed by the limma   package to analyze and experiment with two conditions  using Mouse Gene 1.0-ST chips and I arrive to different results.

I have been looking online and found that at least for the  for the Mouse Gene 1.1-ST the oligo package is preferred, but not anything clear for Mouse Gene 1.0-ST . 

I attach below my code and session info:

A) For running affy:

library(affy)
library(pd.mogene.1.0.st.v1)
library(mogene10sttranscriptcluster.db)

cellist=list.celfiles(full.names=T)
cellistD14=grep("CD1...14",cellist,value=T)
esetD14<- justRMA(filenames=gsub("\\./","",cellistD14))

B) For runnign oligo:

library(oligo)
library(pd.mogene.1.0.st.v1)
library(mogene10sttranscriptcluster.db)

cellist=list.celfiles(full.names=T)
cellistD14=grep("CD1...14",cellist,value=T)

rsetD14=read.celfiles(cellistD14)
esetpD14=rma(rsetD14,target="probeset")
esetD14=rma(rsetD14,target="core")


C) Finally running the same analysis:

designD14<-read.delim('designD14.txt')
contrast.matrix=model.matrix(~treatment,data=designD14)
library(limma)
fit  <- lmFit(esetD14, contrast.matrix)
fit <- eBayes(fit,proportion=0.01)

m1=topTable(fit, coef="treatment",number=1e8,adjust.method="BH")
m1=m1[,c("ID","logFC","P.Value","adj.P.Val")]
m1=cbind(m1[,1:2],FCTreat=2**m1[,2],PTreat=m1[,3],adj.PTreat=m1[,4])

> sessionInfo() (This is for the affy run)
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] mogene10stv1cdf_2.11.0               limma_3.14.4                         mogene10sttranscriptcluster.db_8.0.1
 [4] org.Mm.eg.db_2.8.0                   AnnotationDbi_1.20.3                 pd.mogene.1.0.st.v1_3.8.0           
 [7] oligo_1.22.0                         oligoClasses_1.20.0                  RSQLite_0.11.2                      
[10] DBI_0.2-5                            affy_1.36.1                          Biobase_2.18.0                      
[13] BiocGenerics_0.4.0                  

loaded via a namespace (and not attached):
 [1] affxparser_1.30.2     affyio_1.26.0         BiocInstaller_1.8.3   Biostrings_2.26.3     bit_1.1-9             codetools_0.2-8      
 [7] ff_2.2-10             foreach_1.4.0         GenomicRanges_1.10.6  IRanges_1.16.4        iterators_1.0.6       parallel_2.15.2      
[13] preprocessCore_1.20.0 splines_2.15.2        stats4_2.15.2         tools_2.15.2          zlibbioc_1.4.0       

Thank you very much


J Toledo
UPenn
USA

 		 	   		  
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