[BioC] simpleaffy function detection.p.value - bug

Christian.Stratowa at vie.boehringer-ingelheim.com Christian.Stratowa at vie.boehringer-ingelheim.com
Mon Mar 14 12:49:10 CET 2005

Dear BioC people

Sorrowly, until now I did not receive any reply to my former message.
Meanwhile I have compared the output from detection.p.val (simpleaffy) with
the output from mas5calls (affy).
As shown in the two R sessions below, the output from detection.p.val has
the described bug, while the 
output from mas5calls is correct.

# Package "simpleaffy" version 2.01: Bug in present call
> data <- ReadAffy()
> pval <- detection.p.val(data) 
Getting probe level data...
Computing p-values
Doing PMA Calls
> pval.c <- pval$call
> pval.p <- pval$pval
> pval.pc <- cbind(pval.p,pval.c)
> pval.ord <- pval.pc[order(as.double(pval.pc[,1])),]
> pval.ord[1:4,]
                V0632.CEL.detection.p.val V0632.CEL.present
AFFX-hum_alu_at "0"                       "P"              
AFFX-BioB-M_at  "4.430552596021e-05"      "A"              
AFFX-BioC-3_at  "4.430552596021e-05"      "A"              
AFFX-BioDn-5_at "4.430552596021e-05"      "A"              

# Package "affy" version 1.5.8: correct present calls
> data <- ReadAffy()
> pres <- mas5calls(data)
Getting probe level data...
Computing p-values
Making P/M/A Calls
> pres.c <- exprs(pres)
> pres.p <- se.exprs(pres)
> pres.pc <- cbind(pres.p,pres.c)
> pres.ord <- pres.pc[order(as.double(pres.pc[,1])),]
> pres.ord[1:4,]
                V0632.CEL              V0632.CEL
AFFX-hum_alu_at "0"                    "P"      
AFFX-BioB-M_at  "4.40550144861514e-05" "P"      
AFFX-BioC-3_at  "4.40550144861514e-05" "P"      
AFFX-BioDn-5_at "4.40550144861514e-05" "P"      

It would be great if this bug could be corrected in a newer version of

Best regards
Christian Stratowa

More information about the Bioconductor mailing list