Question: rma and brightness of exon arrays
0
gravatar for Rob Dunne
7.2 years ago by
Rob Dunne230
Rob Dunne230 wrote:
Hi, I am using rma to normalize a set of Affymetrix exon 1.0 ST arrays. I have done this both with the oligo package and with the Affymetrix Power Tools to get equivalent results. I find that the first principal component is completely determined by one of the quality measures, namely pos_control_mean (the mean of the positive control probes as returned by Affymetrix Power Tools) to the extent that pos_control_mean and PCA 1 have an R^2 of 0.93. There is no sign of any outliers. It appears to me that the rma normalization is not removing the brightness effect at all. I find this surprising. Is this what other people are seeing? I am regressing the normalized data on the pos_control_mean and doing further analysis on the residuals. Bye R
oligo • 421 views
ADD COMMENTlink written 7.2 years ago by Rob Dunne230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 153 users visited in the last hour