User: tamsyn.derrick

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Posts by tamsyn.derrick

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DEseq2 design with paired individuals at two timepoints, two groups and two responses
... Hi,  Please can I check my experimental design? I want to be sure it is appropriate for my data/questions. I am also confused that some apparently quite large differences between groups are not statistically significant.  I have 96 samples in total: 48 samples from baseline and 48 samples at 1 mon ...
deseq2 multiple factor design paired samples multiple time points written 2.4 years ago by tamsyn.derrick0 • updated 2.4 years ago by Michael Love26k
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Comment: A: DESeq2 independent filtering not working
... Dear Michael,  Thanks very much for your quick response.  Before analysing these data myself in R I used an online platform to perform the same analysis, which uses DESeq2 behind the scenes. The results from the online platform were quite different and the two top hits from my analysis were set to ...
written 2.5 years ago by tamsyn.derrick0
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DESeq2 independent filtering not working
... Hi, I am analysing my gene expression data with DESeq2 (v1.16.1). I have 12 samples in each of the two groups I am comparing. Some genes have been set to 0/NA by independent filtering, however my top 2 most differentially expressed genes have read counts of 0 in every sample except one (where the ...
deseq2 independent filtering cookscutoff written 2.5 years ago by tamsyn.derrick0

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