## User: Ahdee

Ahdee40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
4 weeks, 1 day ago
Joined:
4 years, 1 month ago
Email:
s********@gmail.com

#### Posts by Ahdee

<prev • 42 results • page 1 of 5 • next >
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... 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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... 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 ...
written 8 weeks ago by Ahdee40 • updated 8 weeks ago by Gordon Smyth39k
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... 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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... 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 ( ...
written 3 months ago by Ahdee40 • updated 3 months ago by Gordon Smyth39k
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... 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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... 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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... 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 ...
written 5 months ago by Ahdee40 • updated 5 months ago by James W. MacDonald51k
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... @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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... 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" ...
written 6 months ago by Ahdee40 • updated 6 months ago by thokall160

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