User: lkianmehr

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lkianmehr0
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Posts by lkianmehr

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Problem with writing CollapseReplicates command
... Hello, I think have problem with writing this command, could you please explain where went wrong exactly with collapseReplicates command? thanks in advance   gr <- factor(c(rep("Dnmt2_ND", 2), rep("Dnmt2_NF", 2), rep("Dnmt2_HD", 2), rep("Dnmt2_HF", 2))) colData <- data.frame(group=gr, typ ...
deseq2 written 7 weeks ago by lkianmehr0 • updated 7 weeks ago by Michael Love19k
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Comment: C: how do compare with DESeq2
... data points (samples) are projected onto 3D plane. most of smples of 4 groups concentrate together and on  PC1 axis, samples of 1 of groups has been separated from each other. ...
written 8 weeks ago by lkianmehr0
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Comment: C: how do compare with DESeq2
... Hi, yes, I have. I made 5 groups to compare,  as below gr <- factor(c(rep("WND", 12), rep("DND", 4), rep("WHF", 4), rep("DHF", 4))), then I made contrast between each two group separately, like this: dif <- data.frame(results(cds, contrast = c("group", "DHF", "DND"))) and tried to find up ...
written 8 weeks ago by lkianmehr0 • updated 8 weeks ago by Michael Love19k
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how do compare with DESeq2
... Hello to all, I am starting to do DGE analysis with DESeq2 with a small example, as a first experiment I am going to compare two groups as example with DESeq2. I have two groups (ND and NF) and there 2 samples in each one (ND1 and ND2 in ND group, NF1 and NF2 in NF group). theses samples are COUNT ...
deseq2 written 9 weeks ago by lkianmehr0 • updated 9 weeks ago by Michael Love19k

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