User: govindrajuk17

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Posts by govindrajuk17

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Comment: C: Design matrix and contrast formation in edgeR for DE analysis
... Dear Aaron, Thank you very much for clarifying my doubts. Will update my edgeR to latest version and repeat the analysis with similar commands mentioned above. Hope it works this time..:) Regards, Govindraj Chavan   ...
written 25 days ago by govindrajuk170
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Comment: C: Design matrix and contrast formation in edgeR for DE analysis
... Dear Aaron, Thanks a ton for quick feedback. I am using edgeR version 3.16.5 as you can see below in session info output: > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-slackware-linux-gnu (64-bit) Running under: Slackware 14.2 locale:  [1] LC_CTYPE=en_US       LC_NUMERIC=C      ...
written 25 days ago by govindrajuk170
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Comment: C: Design matrix and contrast formation in edgeR for DE analysis
... Dear Aaron, Sorry to bother you again. I have one more query regarding same experimental setup described in previous question. In brief, I have three factors as described below: Factor1: Populations(levels=4 (pop1, pop2, pop3 & pop4)). Factor2: Acute stress experiment (levels=2 (control & ...
written 26 days ago by govindrajuk170
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Comment: C: Design matrix and contrast formation in edgeR for DE analysis
... Dear Aaron, Thank you for quick response and confirming my strategy for setting up design matrix  and contrast parameters. Regards, Govindraj Chavan ...
written 5 weeks ago by govindrajuk170
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Design matrix and contrast formation in edgeR for DE analysis
... Hi everyone, I am beginner in edgeR and RNA-seq data analysis, so I need your guidance to set up proper design matrix and contrast for my research questions. I have 64 RNA-seq samples (all biologically independent) from four different populations of same species, which were collected from two diffe ...
edger written 5 weeks ago by govindrajuk170 • updated 5 weeks ago by Aaron Lun15k

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