[BioC] Matchprobe package

[Nathan Salomonis]

Hi Wenqiong,

Thanks for you suggestion.  I haven't had much time to devote to this yet,
but importing the txt file as you suggest below rather than a zip file still
results in the same error you encountered: 

>>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

As Wolfgang suggested, I may need to try a different function or find
someone more knowledgeable than I about R processes. Did you have column
headers that were different than the standard affy, e.g.:
Probe Set Name, Probe X, Probe Y, Probe Interrogation Position, Probe
Sequence, Target Strandedness?

Best Regards,
Nathan Salomonis

-----Original Message-----
From: Wenqiong Chen [mailto:wenchen at diversa.com] 
Sent: Thursday, September 01, 2005 3:16 PM
To: Nathan Salomonis
Cc: bioconductor at stat.math.ethz.ch; Wolfgang Huber
Subject: RE: [BioC] Matchprobe package

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!
Best,

*************************
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
Huber
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
  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
>>
> 
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


--
Best regards
   Wolfgang

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

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