[BioC] error in mas5calls() for soybean chip

[Jenny Drnevich]

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.


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