User: sina.nassiri

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sina.nassiri70
Reputation:
70
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Location:
Switzerland/Lausanne
Last seen:
3 months ago
Joined:
3 years, 5 months ago
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Posts by sina.nassiri

<prev • 14 results • page 2 of 2 • next >
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Answer: A: SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)
... Aina, You mentioned that you want to proceed with a linear model analysis using "voom" and also referred to your input matrix as "counts", so I'm assuming you have count data in hand. If that's the case, you would want to use svaseq() instead of  sva(). In regard to formulating the full model, I ...
written 2.4 years ago by sina.nassiri70
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Comment: C: GSVA indifferent to 'abs.ranking'
... Here is a demo following the nomenclature of provided example in gsva() help document: # simulating data p <- 10 ## number of genes n <- 6 ## number of samples nGrp1 <- 3 ## number of samples in group A nGrp2 <- n - nGrp1 ## number of samples in group B # study design design <- cbi ...
written 2.4 years ago by sina.nassiri70
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Answer: A: can I extract data for subset of cancer types from GSE62944
... Have you read the vignette? https://github.com/Bioconductor/GSE62944/blob/master/vignettes/GSE62944.Rmd There is an example on subsetting data for Low Grade Glioma (LGG), which you can easily modify for other cancer types. # metadata on cancer types phenoData(tcga_data)$CancerType # subset the e ...
written 2.4 years ago by sina.nassiri70
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GSVA indifferent to 'abs.ranking'
... Dear GSVA community, I was playing with the package and noticed that my results are indifferent to abs.ranking argument in the gsva() function. After carefully examining all related documents (original publication by Hanzelmann et al., package vignette, as well as source code), it appears to me tha ...
gsva abs.ranking written 2.4 years ago by sina.nassiri70 • updated 2.4 years ago by Robert Castelo2.3k

Latest awards to sina.nassiri

Great Question 11 months ago, created a question with more than 5,000 views. For Single Sample GSEA (ssGSEA) and dynamic range of expression
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Single Sample GSEA (ssGSEA) and dynamic range of expression
Supporter 2.3 years ago, voted at least 25 times.
Student 2.3 years ago, asked a question with at least 3 up-votes. For GSVA indifferent to 'abs.ranking'
Scholar 2.3 years ago, created an answer that has been accepted. For A: SVA package - ERROR: nvobj = sva(edata, mod, mod0, n.sv=n.sv)

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