[BioC] Matchprobe package

Wolfgang Huber huber at ebi.ac.uk
Thu Sep 1 23:33:08 CEST 2005

Dear Nathan,

please excuse the delayed reply. The answer is yes. You can import a 
wide variety of probe-description files by adapting the function which 
is given to the  'makeProbePackage' function by the 'importfun' 
parameter. Have a look at the default 'getProbeDataAffy', this is a 
function that works for the "normal" probe_tab files. Its (simple) 
commented source code is available through the source packages 
(.tar.gz). I recommend using this as a template and adapting it.

You can use "options(error=recover)" and the debugging browser of R to 
see what exactly is going wrong with your file. I am afraid it is 
difficult to tell for me from  the information you provide, and I 
suppose with a little bit of basic R knowledge (maybe ask a local guru) 
you should be able to trace this down.

  Best wishes

> 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
>>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:
>>>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",
>>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!
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Best regards

Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

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