[BioC] makeProbePackage() error custom array with only PM probes

[James W. MacDonald]

Hi Hans,

Hans van Leeuwen wrote:
> Hi,
>  
> We would like to use gcrma for our custom Affymetrix array (no mismatch
> probes; only perfect match probes). I have successfullly created the CDF
> package in Bioconductor. Now I need to create the probe package with the
> function makeProbePackage().
>  
> I executed the following command:
>  
> makeProbePackage("ourchip", datafile="ourchip_probeSequence_6cols.txt",
> outdir= getwd(), maintainer="our name<ouremail at ucdavis.edu>",
> version="0.0.1", species="Our species", check=FALSE, force=TRUE,
> quiet=FALSE)
>  
> Note: I did experiment with the parameters 'check, 'force' and 'quiet', but
> it gave the same result. The output was as follows:
>  
> Importing the data.
> Error in rep.default(NA, max(pm1, mm1, pm2, mm2)) : 
>         invalid number of copies in rep()
>  
> I also tried calling the getProbeDataAffy() function explicitly, like this:
>  
> makeProbePackage("ourchip", getProbeDataAffy("ourchip",
> "ourchip_probeSequence_6cols.txt", pkgname=NULL, comparewithcdf=TRUE),
> outdir= getwd(), maintainer="our name<ouremail at ucdavis.edu>",
> version="0.0.1", species="Our species", check=FALSE, force=TRUE,
> quiet=FALSE)
>  
> But it resulted in the same error. I have searched online and in the
> Bioconductor archives for this error, and the only thread was this one:
> https://stat.ethz.ch/pipermail/bioconductor/2005-September/010249.html
>  
> Unfortunately, no solution was suggested in that thread.

Actually a solution _was_ suggested - take getProbeDataAffy() and modify 
it so it will work with a chip that has no MM probes.

>  
> Does anyone know what the problem is, and how this can be solved? I suspect
> that it has to do with the input file that I have created. However, I used
> the example templates from Bioconductor, so in theory it should be okay. I
> have six columns in my file, with the following headers:

The problem is that getProbeDataAffy() expects a conventional PM/MM 
chip, and so is erroring out when there are no MM probes.


>  
> Probe Set Name
> Probe X
> Probe Y
> Probe Interrogation Position
> Probe Sequence
> Target Strandedness
>  
> The header fields, and all the data, is seperated with tabs. Each row has
> data for one probe; rows are seperated by a newline character. Within the
> header fields there are spaces.
>  
> Is the problem related to the fact that our array does not have mismatch
> probes? Can gcrma() be used with arrays that do not have mismatch probes?

Theoretically yes, if you have either enough control probes that you 
want to use as substitutes for the MM probes, or if there are enough PM 
probes that have very low binding. This has been discussed on this list 
in the past, and I am certain you could find the thread by searching.

Best,

Jim


>  
> I would be very grateful if someone can help with this.
>  
> Thank you.
>  
> Hans
>  
> 
>  
> 
> ____________________________________
> 
> Hans van Leeuwen, Ph.D.
> 
> University of California, Davis
> 
> 
>  <http://pgfmars.ucdavis.edu/~hleeuwen/> 
> 
>  
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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