User: Ahdee

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Ahdee40
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40
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New User
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United States
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1 day, 17 hours ago
Joined:
3 years, 11 months ago
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Posts by Ahdee

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Comment: C: How to create two columns for model matrix used in limma?
... thanks Gordon, out of curiosity do you know why the model.matrix would deliberatly combine the 3rd coef to one column? ...
written 13 days ago by Ahdee40
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How to create two columns for model matrix used in limma?
... Sorry this is a bit of silly question but its been bothering me a bit. So suppose I have a dataframe as such and want to compare gender or drug. df = data.frame ( gender = c("m","m","f","m","m","f"), drug = c("D1","D2","D1","D2","D1","D2") ) gender = factor ( ...
limma edger written 5 weeks ago by Ahdee40 • updated 5 weeks ago by Gordon Smyth38k
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Comment: C: Limma model design: is it better to just build a separate design for each specif
... Thanks James and Gordon! This is very reassuring - I been using single models ( that is analyzing everything together and using contrast to parse out the different comparison ) however started to freak out mostly because the logfc were different. I though that logFC was simply calculated from the j ...
written 3 months ago by Ahdee40
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Comment: C: Limma model design: is it better to just build a separate design for each specif
... Thanks James, I should be more specific. This is for an RNA-seq that has been TMM normalized and voom. I'm using voom as the input. So in general what you are saying is that leaving everything as a single model and defining the contrast is "better" but only if the variance between the samples are n ...
written 3 months ago by Ahdee40
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Limma model design: is it better to just build a separate design for each specific comparison?
... Hi suppose I have these 3 groups, a b and c. data= c ( rep("a", 3), rep("b",3), rep("c",3) ) mm = model.matrix(~0 + data ) colnames( mm ) = c("a","b","c") makeContrasts( avsb = a - b, levels=mm) a b c 1 1 0 0 2 1 0 0 3 1 0 0 4 0 1 0 5 0 1 0 ...
limma written 3 months ago by Ahdee40 • updated 3 months ago by James W. MacDonald51k
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Comment: C: Why does limma voom E value give different result than the voom object
... @thokall oh yes that right. I read it more carefully now whereby I thought previously that the E value were not only normalized but weighted as well, my bad, thanks! ...
written 4 months ago by Ahdee40
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Comment: C: Seurat 2.3.4 installation
... Hi you could also install directly from github. However first you need to `remove.packages("Seurat")` then make sure that you have install.packages("devtools") library(devtools); devtools::install_github(repo = 'satijalab/seurat', ref = 'release/2.4', dependencies=T) make sure to rest ...
written 4 months ago by Ahdee40
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Why does limma voom E value give different result than the voom object
... Hi so I notice something interesting. data <- voom(x, plot=T, design = design2) vfit <- lmFit(data) vfit <- eBayes(vfit) topTable(vfit,coef=2,sort.by="P") vfit <- lmFit(data$E, design = design2) vfit <- eBayes(vfit) topTable(vfit,coef=2,sort.by="P" ...
limma voom rna-seq written 4 months ago by Ahdee40 • updated 4 months ago by thokall160
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Is there a package to convert DNA coordinates to Cytogenetic location?
... Hi I was wondering if there is package to draw chromosome and/or list out cytogenetic locations based on DNA location. For example here is hg19, chr15:69,373,210-69,373,239. thanks! A ...
annotation coordinates cytogenetic written 5 months ago by Ahdee40
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Help with mapping Kegg hsa01100 using pathview
... Dear all, recently I did an enrichment analysis showing that my RNA.seq data is enriched for the global pathway hsa01100, however on trying to plot this with pathview it does not seem to highlight the genes. I found a similar post previously but its not exactly what I wanted since I'm interested i ...
pathview kegg pathway written 6 months ago by Ahdee40

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