[BioC] ath1121501probe_1.0 error (was GCRMA missing value error)

James MacDonald jmacdon at med.umich.edu
Fri Feb 13 18:44:18 MET 2004

I have made the modified probe package and contributed it. As soon as
Jeff gets it up on BioC, you should be able to download it. Please let
me know if it works (I know the probes have been removed, but don't have
any ath1 cel files to test it with).



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> "Matthew  Hannah" <Hannah at mpimp-golm.mpg.de> 02/13/04 11:28AM >>>
Right I've (with help - thanks Robert, Jean) sorted out what the
problem with the 
ATH1-121501_probe_tab.zip file is - it contains 4 additional control
which total 43 probes.
The extra probesets are
AFFX-r2-At-Actin-3_at (11)
AFFX-r2-At-Actin-5_at (11)
AFFX-r2-At-GAPDH-3_at (11)
AFFX-r2-At-Ubq-5_s_at (10)

So this brings me back to my original query which was that I couldn't
get the
matchprobes package to work on my computer (see other post). So, as the

ath1121501probe_1.0 package is wrong is it possible for someone to
remove the 
probesets listed above from the ATH1-121501_probe_tab file and make a
new probe 
package available for download. I would email the file I've modified
myself but
our institute blocks files >4MB!!!). Alternatively anymore suggestions
on how I 
could get matchprobes to work might help.

Also in my emails with robert he suggested to make a general function
that could 
be used by others to compare the probe sequence file and the cdf file
(or perhaps 
even cel files) which would be a useful addition.

I'd love to be able to do this but my R skills are sadley lacking
(hence all the
questions). But before you all volunteer (?) isn't this done to some
degree already
in the comparewithcdf argument in the getProbeDataAffy function in the
package? Although evidently from the ATH1 case errors can slip

And after all this I still haven't got my gcrma done that I thought
would be a simple
task when I started it over a week ago - anyone would think it was an
unlucky day ;-)


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