Removing control probes from hugene20st arrays

Question

[hakimelakhrass]

Hello,

I am trying to remove the control probes from my data. These are the 'new' affy hugene20st array. The probe IDS and all the other IDS are just numbers. Using this command to remove the genes with low variances should also remove controls but because AFFY is not in the name anymore it does not work.

normData.filtered <- nsFilter(normData, require.entrez=FALSE, remove.dupEntrez=FALSE,feature.exclude="^AFFX")

Any idea how to remove them automated through a function. Or will I have to script it? Thank you!

Answer 1

[Kevin Blighe]

Hey,

You may want to take a look at this thread where a similar question was asked: A: Control probe sets in Affymetrix ST microarrays