User: Matt

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Matt0
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Posts by Matt

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Comment: C: Normalization in DESeq2
... Thanks for responding. We were also concerned about the appearance of the "extreme" example plot, and no, we did not specify our own control genes. My suspicion is more that we have a situation where the transcriptome of this organism was not well-represented in both conditions - we'll certainly inv ...
written 5 months ago by Matt0 • updated 5 months ago by Michael Love19k
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Comment: C: Normalization in DESeq2
... I'm tagging onto this as I have a similar question. Hope this is the right place to ask it. I'd like to follow up with the idea of when a MA plot skew is "too much" for the DESeq2 size factors calculation to handle and what, if anything, can be done about that. I'll preface by saying that we tried t ...
written 5 months ago by Matt0 • updated 5 months ago by Michael Love19k
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Comment: C: DESeq2 normalization prior to identification of highly-expressed functional cate
... Thanks again for the clarification. Using an external package and tximport doesn't fit our current workflow but may as we evolve our analysis strategy. As for your previous recommendations for using TPM to compare genes your advice is well-taken. On Fri, Jan 6, 2017 at 3:41 PM Michael Love [bioc] & ...
written 20 months ago by Matt0
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Comment: C: DESeq2 normalization prior to identification of highly-expressed functional cate
... Mike, Thanks. I agree on further consideration that TPM is the appropriate method for comparing different genes within a given library. As for your recommendation on the various software packages and tximport, you don't mean that you are importing TPM as the primary data type for DE analysis, right ...
written 20 months ago by Matt0
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DESeq2 normalization prior to identification of highly-expressed functional categories
... I've been using DESeq2 for differential expression analysis of microbial (meta)transcriptomic datasets and have been very happy with its performance. I've started to overlay pathway analyses onto these differential expression results to identify functional groupings of genes (via KEGG or SEED) that ...
normalization deseq2 pathway analysis order written 20 months ago by Matt0 • updated 20 months ago by Michael Love19k

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