[BioC] error in ygs98cdf environment?

Straubhaar, Juerg Juerg.Straubhaar at umassmed.edu
Fri Dec 3 20:35:13 CET 2004

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" "AFFX-YER022w3_at"
[5] "AFFX-YER022wM_at" "AFFX-YER022w5_at" "AFFX-YER148w3_at" "AFFX-YER148wM_a"
[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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