[BioC] error in mas5calls() for soybean chip

[James W. MacDonald]

Hi Jenny,

Jenny Drnevich wrote:
> Hi all,
> 
> I've run into some sort of error or bug when trying to get Affy's 
> present/marginal/absent calls for  Affy's soybean array. I've traced the 
> error to this part of mas5calls.AffyBatch():
> 
> calls <- sapply(p, function(y) {
>          if (y < alpha1) {
> 
> 
> According to Benjamin Otto's reponse 
> (https://stat.ethz.ch/pipermail/bioconductor/2006-January/011568.html) to 
> the exact same error message for  HU6800 arrays, specifying alpha1= and 
> alpha2= in the call to mas5calls() should work, but it doesn't for soybean 
> arrays (all codes & output at the bottom). I'm actually not surprised that 
> it doesn't work, because these are the defaults in the internal function 
> mas5calls.AffyBatch() that's called.  Is problem this related to similar 
> problems with the qc() function from simpleaffy not working for some array 
> types? I'll try the solution suggested in 
> https://stat.ethz.ch/pipermail/bioconductor/2006-April/012655.html, but 
> mas5calls is part of the affy package, and I didn't see where functions 
> from simpleaffy were called.

This problem isn't related to anything in simpleaffy. I am betting that 
there are some NAs in the p list that is returned from the call to 
'DetectionPValue' (immediately preceding the code snippet you give 
above). Without actually having any soybean arrays to play with, I 
cannot confirm this, but you could by stepping through the code using

debug(mas5calls.AffyBatch)
mas5calls(rawdata[,1:5])

when you get to the point that the 'p' list is made, you can dump it 
into your .GlobalEnv using

p <<- p

and then quit the debugger (using Q). You could then do something like

sum(sapply(p, is.na))

to see how many (or if) there are any NAs in there. You could also 
figure out which probesets are returning the NAs, and take a look at 
them using the PM() accessor to see if you can tell what the problem 
might be.

Any information you might be able to give could be helpful in debugging 
this error.

Best,

Jim


> 
> 
> Thanks,
> Jenny
> 
>  > rawdata
> AffyBatch object
> size of arrays=1164x1164 features (317565 kb)
> cdf=Soybean (61170 affyids)
> number of samples=30
> number of genes=61170
> annotation=soybean
> 
>  > PMAcalls <- mas5calls(rawdata[,1:5])
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in if (y < alpha1) { : missing value where TRUE/FALSE needed
> 
>  > PMAcalls <- mas5calls(rawdata[,1:5],alpha1=0.04,alpha2=0.06)
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> Error in if (y < alpha1) { : missing value where TRUE/FALSE needed
> 
> 
>  > sessionInfo()
> R version 2.2.1, 2005-12-20, i386-pc-mingw32
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
>     soybeancdf         made4 scatterplot3d          ade4  affyQCReport
>       "1.10.0"       "1.4.0"      "0.3-24"       "1.4-0"       "1.8.0"
>     simpleaffy    genefilter      survival    reposTools       affyPLM
>        "2.4.2"       "1.8.0"        "2.20"       "1.8.0"       "1.6.0"
>       affydata         limma         gcrma   matchprobes          affy
>        "1.6.0"       "2.4.7"       "2.2.0"       "1.2.1"       "1.8.1"
>        Biobase       RWinEdt
>        "1.8.0"       "1.7-4"
> 
> 
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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