User: gthm

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gthm0
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Posts by gthm

<prev • 24 results • page 1 of 3 • next >
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Comment: C: CSAW: Error: could not find function "normOffsets"
... it works after i upgrade everything to latest versions. ...
written 23 months ago by gthm0
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Saving the CSAW results to file
... I am trying to use csaw, but I have not spent enough time on reading documentation as I am in little hurry. I would like to know how should I save the csaw results to a file. I could see the window number in etable but I can't make out which window it is actually (chrom, pos etc). Here is my code: I ...
edger csaw written 23 months ago by gthm0 • updated 23 months ago by Aaron Lun17k
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Comment: C: CSAW: Error: could not find function "normOffsets"
... I just did: source("https://bioconductor.org/biocLite.R") biocLite("csaw") ...
written 23 months ago by gthm0
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Comment: C: CSAW: Error: could not find function "normOffsets"
... One thing I did is to copy paste the entire function from github https://github.com/Bioconductor-mirror/csaw/blob/master/R/normOffsets.R  and it seems to be working. ...
written 23 months ago by gthm0
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CSAW: Error: could not find function "normOffsets"
... I am trying to run csaw but I am getting the following error: Error: could not find function "normOffsets". I could not see it either in the functions available. > library(csaw) Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel ...
chipseq edger csaw written 23 months ago by gthm0 • updated 23 months ago by Aaron Lun17k
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Comment: C: design for glm for edgeR
... what would happen if I just use  treat <- c(rep(c("T"),each=9), rep(c("C"),each=6)) and leave out the subgrouping in the analysis ? Just ignoring the subgroups ? ...
written 23 months ago by gthm0
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design for glm for edgeR
... I would like to compare the DE genes between Treatment (T) vs Control (C). The Treatment and controls have subgroups ( which are minor variants of treatments/controls ), so I would expect some genes to show differential expression between different subgroups of treatment/control, but I am only inter ...
edger written 23 months ago by gthm0 • updated 23 months ago by Michael Love15k
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Comment: C: Help in design matrix for edgeR/DESEQ
... Yes, I'm sorry for all the confusion. We have treated the six biological replicates with two minor variants of a drug (3+3). Hence, I would expect some genes to be differentially regulated between a and b, which I would like to ignore  and compare only treated vs untreated. ...
written 23 months ago by gthm0
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Comment: C: Help in design matrix for edgeR/DESEQ
... they all are biological replicates. ...
written 23 months ago by gthm0
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Comment: C: Help in design matrix for edgeR/DESEQ
... Thanks for the reply. I have updated my question. A vs B were confusing. I mean to say with in treated/untreated , I would expect some DE Genes between A vs B and C vs D, which I would like to ignore and look for DE genes between only treated vs untreated. ...
written 23 months ago by gthm0

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Popular Question 22 months ago, created a question with more than 1,000 views. For Multi factor design edgeR/Deseq2

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