[BioC] error in matchprobes package

James W. MacDonald jmacdon at med.umich.edu
Wed Sep 12 15:33:00 CEST 2007

Hi Yan,

yzhang at vbi.vt.edu wrote:
> When I use makeProbePackage function in newest version matchprobes
> package(1.8.1), I got the following error message:
>> makeProbePackage("ehis1a520285f",version="1.0",species="ehis",maintainer="yanzhang<yzhang at vbi.vt.edu>",build=FALSE,
> check=FALSE, force=True)
> Importing the data.
> Error in rep(NA, max(pm1, mm1, pm2, mm2)) :
>         invalid 'times' argument
> In addition: Warning messages:
> 1: NAs introduced by coercion in: as.integer.default(dat[[2]])
> 2: NAs introduced by coercion in: as.integer.default(dat[[3]])
> 3: NAs introduced by coercion in: as.integer.default(dat[[4]])

The error comes from code that compares the probeset IDs from the probe 
package with the cdf package, and IIRC this happens when you have a 
PM-only chip. Is this chip PM-only?

The warnings come from an unfortunate change that was made to 
getProbeDataAffy() that I have fixed in the devel version (and have no 
idea right now why I didn't push to the release as well...). The problem 
stems from the fact that you are reading in the whole probe_tab file, 
including the header. When the (x,y) coordinates and probe interrogation 
position data are coerced to integer, the first value for each is 
character, which is coerced to a NA.

The release branch is no longer being built, so I cannot push a fix that 
will end up being available. The easiest thing for you to do is upgrade 
your R to 2.6.0 alpha and use the devel version of matchprobes.



> I don't have this problem if I use old version(1.0.22).
> Anyonne knows what cause this?
> best
> yan
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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