User: bruno.saubamea

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Posts by bruno.saubamea

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Answer: A: tximport output files files from salmon
... You might need tximport and then (for example) DESeq for the differential analysis. You shoud have a look at : https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html     ...
written 10 months ago by bruno.saubamea0
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Comment: C: Systematic underestimation of log2fc values in DESeq?
... I'll try this!   ...
written 11 months ago by bruno.saubamea0
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Comment: C: Systematic underestimation of log2fc values in DESeq?
... sorry, this is the link to the original image http://imgur.com/E6aseuu ...
written 11 months ago by bruno.saubamea0
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Answer: A: Systematic underestimation of log2fc values in DESeq?
... Below are the MAplots with shrunken and unshrunken LFCs (or for better resolution). I'm not sure whether they look OK... ...
written 11 months ago by bruno.saubamea0
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Answer: A: Systematic underestimation of log2fc values in DESeq?
... OK. The problem might come from the estimated size factors because my sample A is significantly contaminated (might be as high as 50% of total cells) by blood cells while my sample B is highly pure (A and B are 2 distinct but closely related cell types). Thus the size factors might not adequately no ...
written 11 months ago by bruno.saubamea0
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Answer: A: Systematic underestimation of log2fc values in DESeq?
... I was not aware of this normalization. I will search the forum. In my data mean(lfc) and median(lfc) are about -0.25. Is it coherent with the fact that the distribution is normalized? ...
written 11 months ago by bruno.saubamea0
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Comment: C: Systematic underestimation of log2fc values in DESeq?
... I'm aware of the shrinkage. If I'm correct it is included by default in DESeq 1.14.1 but the unshrunken LFC can be retrieved by adding addMLE=TRUE in the calling of results(dds). So I compared the shrunken and unshrunken LFC but the problem remains. In fact the shrk LFC distribution has the ...
written 11 months ago by bruno.saubamea0
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Systematic underestimation of log2fc values in DESeq?
... Dear all, I suspect log2fc values in our DGE study using DESeq2 (DESeq 1.14.1)  to be systematically  understimated (say 2 instead of 2.5, 0 instead of 0.5, -2 instead of -1.5) I understand that my question is rather general but are there any reasons that could lead DESeq to underestimate fc? I ...
deseq2 written 11 months ago by bruno.saubamea0
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Answer: A: generating an order ranked gene list
... Yes it was that simple. Thank you ...
written 11 months ago by bruno.saubamea0
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Answer: A: eroor mssage using gseKEGG
... That's it! Thank you ...
written 11 months ago by bruno.saubamea0

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