User: sina.nassiri

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sina.nassiri40
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Switzerland/Lausanne/EPFL
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2 weeks, 4 days ago
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1 year, 2 months ago
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Posts by sina.nassiri

<prev • 6 results • page 1 of 1 • next >
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Answer: A: DESeq2 DESeqDataSetFromTximport design formula
... Not sure what you mean by "paste together whichever factors I want to compare further down the line", but the problem with matrix not being full rank is that the columns for condition and eya1six1 are linearly dependent in the design matrix, i.e. condition and eya1six1 are confounding. What's your e ...
written 6 weeks ago by sina.nassiri40
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Comment: C: GSVA indifferent to 'abs.ranking'
... Dear Dr. Castelo, Thank you for the feedback. I upgraded to the latest version (1.24.1) and reran the example above. Results from abs.ranking=TRUE and abs.ranking=FALSE are no longer identical, but I'm still confused about the utility of abs.ranking. Let's return to above example in which set4 is a ...
written 6 weeks ago by sina.nassiri40
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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 6 weeks ago by sina.nassiri40
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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 7 weeks ago by sina.nassiri40
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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 7 weeks ago by sina.nassiri40
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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 7 weeks ago by sina.nassiri40 • updated 7 weeks ago by Robert Castelo2.0k

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Scholar 4 weeks 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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