User: takumima

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takumima10
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Posts by takumima

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Comment: C: Paired analysis (tumor vs normal) at three different conditions with EdgeR
... Thank you @Aaron Lun. I made two more comparisons, namely conditions 2 and 3 *versus* the cond1: cond1vscond2=(groupcond1.T-groupcond1.N)-(groupcond2.T-groupcond2.N) cond1vscond3=(groupcond1.T-groupcond1.N)-(groupcond3.T-groupcond3.N) So, when I use `geneQLFT = glmQLFTest(geneQLF, contras ...
written 9 months ago by takumima10
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Paired analysis (tumor vs normal) at three different conditions with EdgeR
... Hi all, I have 18 samples, 3 tumor and 3 paired normal tissue samples, belonging to the same individual, at three different conditions, each in three replicates. $df sample group tissue sample1-T-cond1 cond1 T sample1-T-cond1 cond1 T sample1-T-cond1 cond1 T ...
edger design de matrix written 9 months ago by takumima10 • updated 9 months ago by Aaron Lun25k
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Comment: C: Differential profile for only one normal - tumor pair
... Thank you, Gordon, for your suggestions. Your solution seems to work! However, I'm not sure if my code returns the list of DEGs in the tumour sample. This because by performing the analysis on a publicly available dataset, my gene of interest is up-regulated, exactly the opposite of what is reporte ...
written 17 months ago by takumima10
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Differential profile for only one normal - tumor pair
... Hi all, I analysed the list of DEGs in 10 tumour-normal pairs (without replicates), with edgeR. I used the paired design design = model.matrix(~Patient+Tissue) Now, I would like to get the list of differentially expressed genes for each tumour-normal pair, individually. The aim is to get the pat ...
edger paired design degs written 17 months ago by takumima10 • updated 17 months ago by Gordon Smyth39k

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