Interaction categorical/continuous variable DESeq2
Hugo Varet <[email protected]> Mon, 15 Sep 2014 15:41:24 +0200
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <[email protected]> |
Dear list, dear Mike Love, I am using DESeq2 to model counts from an unusual type of experiment and I have a question about the strategy I employed. The experiment consisted in sequencing 33 samples for which we have the following information: - group (16 samples from group A and 17 from group B) - a continuous variable X almost uniform (variable of interest) I have to add the group to the design formula because I know it has a strong effect on the counts. Then, as my goal is to detect genes which vary with the continous variable X in the same way within both groups A and B, I want to exclude genes for which there is an interaction between group and X. The design is thus ~ group + X + group:X and I used the following lines to test the interaction: dds <- DESeqDataSetFromMatrix(countData=counts, colData=target, design = ~ group + X + group:X) dds <- estimateSizeFactors(dds) dds <- estimateDispersions(dds) dds <- nbinomWaldTest(dds) res <- results(dds, name="groupB.X") sum(res$padj<=0.05, na.rm=TRUE) hist(res$padj) As I found no significant interaction (the minimum adjusted p-value is about 0.6), I decided to remove the interaction term from the design and to use ~ group + X. I can then test for the coefficients of X. If I do not detect any significant interaction, I think it is due to a lack of power. So, can I use the additive model ~ group + X even if it will not be correct for genes which actually have an interaction? Many thanks in advance, Hugo PS: I am using R 3.1.1 and DESeq2 1.4.5 _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor