Hi Jim and Ken and the rest of the list, Thanks for the debugging suggestions. The problem is indeed with "probe sets" that only have one probe pair; if the PM > MM, then 'DetectionPValue' returns 0, but it PM <= MM then 'NaN' is returned. I was able to get 'mas5calls.AffyBatch' to work by simply adding this one command before the P/M/A calls were made: p[sapply(p,is.na)] <- 1 I'm not sure what's the best way to call P/M/A when there is only one probe pair in a probe set, but perhaps a warning/output could be generated along the lines of "One or more of the probe sets has only one probe pair. Use 'oneProbePair()' to find out which ones". [code is below for a simple function I wrote to get the probe set names]. Or would a warning cause more problems from unnecessary panic? I was surprised that there were 92 "probe sets" on the soybean chip with only one probe pair? I wonder how many other chips actually have single probe pair "probe sets" - as long as PM>MM for all the arrays, mas5calls() would work and you'd never know... Cheers, Jenny oneProbePair <- function(object) { x <- probeNames(object) dups <- unique(x[duplicated(x)]) singles <- setdiff(unique(x),dups) return(singles) } At 01:49 PM 4/18/2006, James W. MacDonald wrote: >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 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >-- >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 > > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should not >be used for urgent or sensitive issues. > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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