User: anou
anou • 0
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Posts by anou
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... 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 17 days ago by
anou • 0
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... 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 23 days ago by
anou • 0
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... 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 27 days ago by
anou • 0
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... 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 27 days ago by
anou • 0
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... 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 ...
written 27 days ago by
anou • 0
• updated 24 days ago by
Gordon Smyth ♦ 35k
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... 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 18 months ago by
anou • 0
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... 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 18 months ago by
anou • 0
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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 ...
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