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User: Ben Gabriel

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Posts by Ben Gabriel

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Comment: C: DESeq2::sizeFactors() function does not output the sizeFactor table.
... Ha! Interesting. Thanks much! So even though (I guess) the normalization factors are calculated using the DESeq2::estimateSizeFactors() from a DESeqDataSet object (either created using a tximport or another input), the result of the estimateSizeFactors() function is stored/accessed differently - de ...
written 12 days ago by Ben Gabriel0
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DESeq2::sizeFactors() function does not output the sizeFactor table.
... Hi everybody, This is a quick question regarding the DESeq2::sizeFactors() function. To my knowledge, and I hope I am right here, this function prints out the size factor table calculated by the DESeq2::estimateSizeFactors() function, or can be used to assign a size factor table to a DESeqDataSet. ...
deseq2 written 13 days ago by Ben Gabriel0 • updated 13 days ago by Michael Love22k
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Comment: C: Strange lfcShrink plot when running DESeq2 workflow
... Hey... Thanks for your quick response... But no... I do not plot the intercept... (below part of my output) > show(dds_design) DF_4 DF_9 DHF_4 DHF_9 1 0 1 0 0 2 1 0 0 0 3 0 1 0 0 4 1 0 0 0 5 0 1 0 0 6 0 0 ...
written 4 months ago by Ben Gabriel0
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Strange lfcShrink plot when running DESeq2 workflow
... Hi everybody, I am producing right now a strange plot while running the DESeq2 workflow when running the command lfcShrink on the DESeqDataSet object (after running the DESeq function). I assume right now that there is an error within my workflow but I can not figure out what the problem. In a nut ...
rnaseq deseq deseq2 rna-seq written 4 months ago by Ben Gabriel0

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