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Old 10-23-2013, 12:03 AM   #1
Junior Member
Location: israel

Join Date: Oct 2013
Posts: 2
Default using DESeq2 for RNA-Seq analysis

Hello All,
i have used the DESeq package for RNA-Seq analysis up until recently.
after discovering the DESeq2 package, i have tried using it for that kind of analysis, and encountered some problems.
1. i have read that the package offers two different statistical testing for differential expression : the "nbinomWalsTest" and the "nbinomLRT", i can't seem to understand fully what is the difference between them and what is the recomanded test using for RNA-Seq analysis.
2. my current data contains 4 conditions, one of them is the control and the other three ate different treatments. when using the nbinomWaldTest i have used the "contrast" option in order to define the specific comparison that i am intreasted in. is there some kind of option like that for the LRT test? since right now i only receive results comparing all conditions to the control.
3. i would like to receive MA plots for my comparisons between different conditions, right now all i was able to receive is the plots of comparing each condition to the control (since those are the results available in the results() function by default)

i general, if anyone has expreience using this tool on RNA-Seq analysis, i would really appritiate any help regarding the steps to take for receiving full results.

thank you very much,
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