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Old 01-19-2015, 11:55 AM   #1
Golsheed
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Default correcting for gene-length and GC-content bias in DESeq2

Hi,
I was wondering whether DESeq2 has a feature to correct for gene-length and GC-content bias simultaneously?
I currently am correcting for GC-content bias using the method explained in DESeq2 manual (i.e., the normalizationFactors matrix). But I need to do correction for gene-length, since I'm trying to find differentially expressed genes between three species. Assuming that L_ij is the length of gene i in condition (subgroup) j, how do I incorporate matrix L along with the normalizationFactors matrix into the data set?
I'd appreciate any help.
Thanks,
Golsheed
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Old 01-19-2015, 01:43 PM   #2
Michael Love
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Are you using CQN? Something to think about is that CQN estimates the GC bias assuming that the genes are the same length across samples. See ?cqn.

What's the distribution of gene length differences, e.g.:

summary(log2(L[,1] / L[,2]))
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Old 01-19-2015, 01:52 PM   #3
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Thanks for the answer. EDASeq is used for that part of the analysis to correct for GC bias.

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Old 01-19-2015, 01:56 PM   #4
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Can I correct for both GC content and gene length with EDASeq and then use the output from EDASeq in DESeq2?

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Old 01-19-2015, 04:09 PM   #5
Michael Love
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That's a question for the EDASeq devels. DESeq2 can take any normalization matrix.

Note that, similar to CQN, the covariates (gene length, GC) are provided as vectors to EDASeq, i.e. one per gene, not a matrix of gene lengths.
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Old 01-19-2015, 04:25 PM   #6
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Thanks a lot. Your response is extremely helpful.

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