[BioC] GCRMA missing value error on ATH1 chip

Zhijin Wu zwu at jhsph.edu
Thu Feb 12 21:56:03 MET 2004

 there seems to be a disagreement on how many pm probes there are on the
chip. This is causing problem in matching the pm intensities with
sequences. I am not sure if this is true for all ATH1 chip...

  After reading in your Cel file into "object",
  pmIndex <-  unlist(indexProbes(object,"pm"))
  #however the probe package gives 251121 pm probe sequences.
  [1] 251121
  right now I am not sure which should be fixed-- whether the probe
package has some redundent sequences that are not PM probes or the
indexProbes missed some pm probes?


On Wed, 11 Feb 2004, Matthew Hannah wrote:

> Hi,
> 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.
> Thanks
> Matt  
> > data <- ReadAffy()
> > esetgcrma <- gcrma(data)
> Computing affinities
> Attaching package 'matchprobes':
>         The following object(s) are masked from package:Biobase :
>          combine 
> ...Done.
> 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
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