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Old 04-09-2013, 06:39 AM   #1
jvelotta
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Location: Connecticut

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Default RNA Seq: differential gene expression with multiple factors

Hello,

I'm looking to assess differential gene expression using Illumina HiSeq reads. I have a two-factor experimental design (three divergent fish populations each treated at two salinities). I would like to assess differential expression using a two-way model - specifically I want to pinpoint genes for which there are significant interaction effects.

Does anyone know if any of the (many) RNA seq tools available can run a model of this kind (probably a generalized linear model) using these data?

Thanks so much.
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Old 04-09-2013, 08:57 AM   #2
kopi-o
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edgeR and DESeq/DESeq2 can do this and yes, they use GLMs. There are probably other packages too but these are the ones that come to mind.
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Old 04-09-2013, 11:37 AM   #3
jvelotta
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Thanks. Any experience with either of these packages? Are there major differences?
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Old 04-09-2013, 11:55 AM   #4
kopi-o
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I'm a satisfied user of both. I would not say there are major differences between them.
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Old 04-09-2013, 02:48 PM   #5
shi
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Another option is limma. You use its lately developed 'voom' function to normalize your data and then you can analyse your data in the same way as analyzing microarray data.
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