[BioC] Matchprobe package

Wenqiong Chen wenchen at diversa.com
Fri Sep 2 00:15:55 CEST 2005

Hi, Nathan:
I was the one who posted the message long time ago which you quoted in
your message. This is the command I tried which worked eventually, which
is, believe or not, much straightforward.
> makeProbePackage("disdiv712a",
datafile="diS_div712a_probeSequenceFile.txt", maintainer = "Joan Chen
<jchen at diversa.com>", version    = "0.0.1", force=TRUE)

Where you only need to supply unzipped txt file of your probe tab file.
You do need to supply the column names in this txt file.
Hope this also works for you!

Wenqiong J. Chen, Ph.D
Bioinformatics Staff Scientist
Diversa Corp.
4955 Directors Place
SD, CA 92121
(O): (858)-526-5334
jchen at diversa.com

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wolfgang
Sent: Thursday, September 01, 2005 2:33 PM
To: Nathan Salomonis; 'bioconductor at stat.math.ethz.ch'
Subject: Re: [BioC] Matchprobe package

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
> Best Regards,
> Nathan
>>I am trying to make probe package with the functions in the
>>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!
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

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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