User: anou

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anou0
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Posts by anou

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Comment: C: edgeR paired samples with blocking
... So I ran the modeling with a second duplicateCorrelation as suggested, and got a corfit$consensus of 0.6093099. I was happy with the results, till I checked the pvalue distribution pvals <- topTable(efit, coef=3, n=Inf)$P.Value sum(pvals <= 0.01)/length(pvals) # 0.1230808 and the   of vm$E ...
written 6 weeks ago by anou0
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Comment: C: edgeR paired samples with blocking
... Thank you for the recommendation Gordon, but why would you not do the normalization based on cpm per sample?  keep <- rowSums(cpm(y)>1) >= 3 ...
written 7 weeks ago by anou0
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Comment: C: edgeR paired samples with blocking
... I'll answer your questions, but first, a rant.  Fair enough and you have a point. I just figured that if the same genes were detected by multiple methods, they were more likely to be identified correctly. I would suggest looking at their expression values directly to see whether it is a modelling ...
written 8 weeks ago by anou0
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Comment: C: edgeR paired samples with blocking
... Thank you for your explanation Aaron and the appropriate section in the guide. I don't have to use edgeR, but as we don't know what outcome we expect, I thought it might be a good idea to do the analysis with three packages (edgeR, DeSeq2 and limma-voom) to compare the resulting genes. I should be ...
written 8 weeks ago by anou0
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edgeR paired samples with blocking
... I have the following experimental design and want to estimate the differences between nonallergic.BPE vs nonallergic.Medium, allergic.BPE vs. allergic.Medium etc. I would like to use patient as a blocking factor patient genotype condition 73644 1 nonallergic Medium 73645 1 ...
limma edger paired samples blocking written 8 weeks ago by anou0 • updated 7 weeks ago by Gordon Smyth36k
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Answer: A: Xps configuration error on Ubuntu 16.04 despite root being installed
... Hi Christian, I have just installed the version 5.34.36, and when I run root its recognising it as well: system > root   *******************************************   *                                         *   *        W E L C O M E  to  R O O T       *   *                                   ...
written 19 months ago by anou0
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Answer: A: Xps configuration error on Ubuntu 16.04 despite root being installed
... Hi Mike, I have installed root 6.10.00. I tried the Ubuntu repository version and installed/configured from source. Root is running, and the header files are in the /include folder... I'm wondering if there is something wrong with the way the systems variable is set? Not sure where the 5.34.30 ver ...
written 19 months ago by anou0
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Xps configuration error on Ubuntu 16.04 despite root being installed
... Hi all, I'm trying to install the xps in R via biocLite('xps') but I'm getting a configuration error: * installing *source* package ‘xps’ ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether ...
xps root tparallelcoord.h written 19 months ago by anou0 • updated 19 months ago by cstrato3.9k

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