[BioC] error in ygs98cdf environment?

Crispin Miller CMiller at PICR.man.ac.uk
Sat Dec 4 13:30:56 CET 2004

There was a typo in the set up file - I've fixed in version 2.05 (which
will appear in the devl branch shortly).  

In the meantime if you want to get under the bonnet, in the package
directory for simpleaffy you'll find a directory: 'data', containing the
file 'qc.probes.tab'. Third line from the bottom you'll find your
probeset; you can fix it in there...


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Straubhaar,
Sent: 03 December 2004 19:35
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] error in ygs98cdf environment?

getAllQCProbes("ygs98cdf") produces the following vector of yeast
control probes on the YG_S98 Affymetrix microarray chip:

[1] "AFFX-YFL039C3_at" "AFFX-YFL039CM_at" "AFFX-YFL039C5_at"
[5] "AFFX-YER022wM_at" "AFFX-YER022w5_at" "AFFX-YER148w3_at"
[9] "AFFX-YER148w5_at"

The 8th component of this vector is missing a 't' at the end. When I use
simpleaffy with gc.affy(AffyBatch) I run into an error:

Error in FUN(X[[8]], ...) : subscript out of bounds

I traced this error to the eighth component of the qc vector above and
the error occurs in the step:

qc.probe.vals <- rbind(c(), (sapply(qc.probenames, function(y) {
        x[y, ]

In debug mode when I edit qc.probenames I don't get an error. 

Juerg Straubhaar
Umass Med

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