[BioC] GCRMA missing value error on ATH1 chip

Matthew Hannah Hannah at mpimp-golm.mpg.de
Wed Feb 11 12:06:38 MET 2004


I seem to get nothing but problems... I have the appropriate probe package
but now when I try to run gcrma I get the error detailed below.

I did a search and the only similar thing I found listed was with the Li-wong
function where it was proposed that it might have something to do with the 
fact that some probesets had only 1 probepair. I've looked at the ATH array and
there are some sets with only 8, 9 or 10 probesets. It does not seem to be a
problem of masks on the CEL files as I've tried it with mulitple CELs from 
different sources (they are all several months old - did I hear something
about a new binary format?).

It must have something to do specifically with the gcrma method as rma(data)
works fine. Any ideas how to overcome this problem, or other people with 
success on ATH1 arrays. I'm using R 1.9devel and latest BioC and gcrma (1.0.2)
on win2k 2Ghz, 1GB RAM.


> data <- ReadAffy()
> esetgcrma <- gcrma(data)
Computing affinities
Attaching package 'matchprobes':

        The following object(s) are masked from package:Biobase :


Adjusting for optical effect..........Done.
Adjusting for non-specific binding.Error in quantile.default(y, Q) : Missing 
values and NaN's not allowed if `na.rm' is FALSE

More information about the Bioconductor mailing list