T-Test And P-Values For Microarray Expression Data

Question

[khan]

Hi all,

I have microarray expression matrix : columns are different cancers and the rows are my gene.

I want to detect the artifcats in my data sets, in other word, I want to see, whether the over-under expression of genes are by chance or they have some biological reasons.

How can I test this with computing P-values and T-test in R ? does anyboy knows R or bioconductor package which are specified for this task?

[Devon Ryan]

Have you normalized your values yet? Have you looked at limma? There have been countless posts here and elsewhere on using R to analyse microarrays.

Answer 1

[Sean Davis]

It sounds like you may want to look at the limma bioconductor package. In particular, the limma user guide is an excellent resource.