[BioC] simpleaffy function detection.p.value - bug solved in version 2.10

[Christian.Stratowa at vie.boehringer-ingelheim.com]

Dear BioC people

Crispin Miller was so kind to inform me that this bug has been solved in
version 2.10, as you can see from the following R session:

# Package "simpleaffy" version 2.10: correct present calls
> 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"      "P"              
AFFX-BioC-3_at  "4.430552596021e-05"      "P"              
AFFX-BioDn-5_at "4.430552596021e-05"      "P"              
> 

Best regards
Christian Stratowa

>  -----Original Message-----
> From: 	Stratowa,Dr.,Christian FEX BIG-AT-V  
> Sent:	Monday, March 14, 2005 12:49
> To:	'bioconductor at stat.math.ethz.ch'
> Cc:	'cmiller at picr.man.ac.uk'
> Subject:	[BioC] simpleaffy function detection.p.value - bug
> 
> 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
> simpleaffy.
> 
> Best regards
> Christian Stratowa
> 
> 
> 
> 
>