DESeq data analysis

[kasutubh]

Hi everyone,

I want to use DESeq for rna-seq analysis. I was trying to work out with the trial data when I ran into problem. I wanted to go for DE after estimating the dispersion with the estimateDispersion function. When I do the nbionomTest I get following error,
Error in nbinomTest(cds, "untreated", "treated") :
For CountDataSets with multivariate conditions, only the GLM-based test can be used.
Why is this happening?
Thanks in advance.

[Wolfgang Huber]

Kasutubh,

most likely you have not followed the example code exactly, but made changes or permutations that led to that error. Note that a file with R code that reproduces the vignette comes with the package and is also available online at http://www.bioconductor.org/packages...tml/DESeq.html (follow the link called "R Script"). I suggest that you first make sure that you can reproduce the vignette; then spend a little bit of time understanding the basics of manipulating data structures in R (see e.g. [1]). Then you can adapt the workflow to your own data.

Hope this helps,
best wishes
Wolfgang

[1] http://www.bioconductor.org/help/cou...Bressanone2012 --> 2012-07-02-Gatto-R-Basics.pdf

[kasutubh]

Hi Wolfgang,

Thanks for your reply. It works now..

Best wishes,

Kaustubh