[BioC] DESeq2: detect significantly increasing across an ordinal variable

[Daniel Brewer (BIO)]

I have an RNASeq dataset that has samples from three conditions: low, medium and high.  What I would like to find is genes that have expression that either increases or decreases with the condition.  I have been using DESeq2 to do differential analysis and so was wondering if there is a way to do this.  I tried to use the log-ratio-test as indicated in the time-series section of the vignette, but that is a  "test for any dierences over multiple time points”.

Any ideas? Thanks

Dan 

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Dr Daniel Brewer
Senior Bioinformatics Officer | Cancer Genetics
School of Biological Sciences | University of East Anglia | Norwich Research Park | Norwich | NR4 7TJ

Tel: +44 (0) 1603 592906 | Email: d.brewer at uea.ac.uk