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

Matthew Hannah Hannah at mpimp-golm.mpg.de
Fri Feb 13 17:28:04 MET 2004

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 probesets 
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 matchprobe 
package? Although evidently from the ATH1 case errors can slip through.

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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