affymetrix Gene expression .soft file processing

Question

[sujasubramanian]

Hello Sean Davis, Can you help me to process .soft gene expression file, i have taken average of both normal and cancerous sample, is this the right way to process the data ,another case same gene is presented in multiple probes, how can i process such multiple cases.

Answer 1

[Sean Davis]

In general, taking the average across samples is not very useful, assuming that you want to perform differential expression. Instead, take a look at a package like the limma package to perform differential expression. As for multiple probes per gene, I tend to leave them as individual probes and not collapse them; doing so is not always the optimal approach, but it is quick and easy.