Hi Wolfgang,

 

I was having the same error as with the user in the thread below.  I have a
custom Affymetrix array (non-commercial) that has no mis-match probes only
perfect match. I have generated a CDF file and run RMA successfully.  I have
also generated a file analogous to the _probe_tab files supplied by
Affymetrix (except I didn't include a Probe Interrogation Position since I
didn't have consensus sequence information - left all values for this column
zero) and compressed it in .gz format. Can I expect to be able to generate a
proper probe package given that there are no mismatch probes?

 

Best Regards,

Nathan

 

 

> Hi,
> I am trying to make probe package with the functions in the "matchprobe"
> package. However, we have modified the cdf file and probe sequence file
> to accommodate the recent update of the in house genome sequence. I have
> successfully created the cdf package with the modified cdf file, and
> everything worked as far as use rma. However, to get the GCRMA work I
> would need to create the probe package where I am having trouble. I have
> checked that all the probe sequences within the cdf file were included
> in the probe sequence file, although the probe sequence file contain
> more sequences than the ones in the cdf file. 
> Here the error message I got:
> 
> 
>>library(matchprobes)
>>makeProbePackage("disdiv712a", getProbeDataAffy("disdiv712a",
> 
> "diS_div712a_probeSequenceFile.txt", pkgname = NULL, comparewithcdf =
> TRUE), maintainer = "XXXX<XXXX at diversa.com
<https://stat.ethz.ch/mailman/listinfo/bioconductor> >", version    =
"0.0.1",
> force=TRUE)
> Error in rep.default(NA, max(pm1, mm1, pm2, mm2)) :
> invalid number of copies in "rep"
> In addition: Warning messages:
> 1: NAs introduced by coercion
> 2: NAs introduced by coercion
> 3: NAs introduced by coercion
> 
> Can anyone please point out what is wrong?
> Thanks in advance!
> 
> wenqiong
> 

 


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