Section 4 in DESeq tutorial covers multiple-factor, but multi-factor is NOT equal to multiple conditions. I believe in real world, more often you have more conditions than just two. Let's say I have a study: 1. 3 conditions: control, treat_1, and treat_2 2. Triplicates in each condition 3. comparisons: a: treat_1 vs control b: treat_2 vs control Questions: how to do it using DESeq? I did google around, search Seqanswrs ..., but still wondering. Thanks, Shanrong

On 16/01/13 05:18, Shanrong Zhao wrote: > > Section 4 in DESeq tutorial covers multiple-factor, but multi-factor is NOT > equal to multiple conditions. > > I believe in real world, more often you have more conditions than just two. > Let's say I have a study: > 1. 3 conditions: control, treat_1, and treat_2 > 2. Triplicates in each condition > 3. comparisons: > a: treat_1 vs control > b: treat_2 vs control > > Questions: how to do it using DESeq? I did google around, search > Seqanswrs ..., but still wondering. If you do not have any factors beyond your more-than-two conditions, you simply call nbinomTest for each comparison, always giving the two conditions you want to compare as second and third argument. Simon