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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4 weeks, 1 day ago
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4 years, 1 month ago
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Posts by Ahdee

<prev • 42 results • page 1 of 5 • next >
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Comment: C: UnProducible error with goana and kegga function
... Thanks Gordon: I don't know why but it seem to be working again. And the same function used yesterday `df = getGeneKEGGLinks ()` seem to be working again. May be it just so happen that the server was back up when you tried it? I don't know but glad its working again. I'm going to store this loca ...
written 8 weeks ago by Ahdee40
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UnProducible error with goana and kegga function
... Hi so I been running many scripts without an issue for both goana and kegga, however just today, the same script with the same input is giving this error. Error in read.table(URL, sep = "\t", quote = "\"", fill = TRUE, comment.char = "", : duplicate 'row.names' are not allowed My g ...
limma goana kegga written 8 weeks ago by Ahdee40 • updated 8 weeks ago by Gordon Smyth39k
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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 10 weeks 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 3 months ago by Ahdee40 • updated 3 months ago by Gordon Smyth39k
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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 5 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 5 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 5 months ago by Ahdee40 • updated 5 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 6 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 6 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 6 months ago by Ahdee40 • updated 6 months ago by thokall160

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