User: sina.nassiri

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sina.nassiri50
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Switzerland/Lausanne
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2 weeks ago
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1 year, 6 months ago
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Posts by sina.nassiri

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Applying sva is compatible with limma duplicateCorrelation?
... I completely agree with you on using full model + SVs, but in this case neither one of "sex","age", and "city" is a variable of interest. Am I missing something here? ...
written 9 weeks ago by sina.nassiri50
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Comment: C: Applying sva is compatible with limma duplicateCorrelation?
... 1) I'd go with the former, because in the latter you're throwing out potentially valuable information about study design. 2) Sure; I missed cell type composition. 3) You are right about svaseq being similar to using sva with v$E; I just double checked the source code. My bad! ...
written 12 weeks ago by sina.nassiri50
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Answer: A: Extracting subclusters from original data
... I'm not familiar with ComplexHeatmap, but if it produces a tree (as resulting from hclust e.g.) you can directly pass it to cutree(). ...
written 12 weeks ago by sina.nassiri50
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Answer: A: Applying sva is compatible with limma duplicateCorrelation?
... In principle, if you don't include 'patient' in the full model (mod) it will be captured by SVA (assuming that it has a significant contribution to the overall variation observed). However, there are a few points to consider: 1- You have already included sex, age, and city in the null model during ...
written 3 months ago by sina.nassiri50
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Single Sample GSEA (ssGSEA) and dynamic range of expression
... Dear ssGSEA users, In ssGSEA, gene expression values for a given sample are rank-normalized, and an enrichment score is produced using the Empirical Cumulative Distribution Functions (ECDF) of the genes in the signature and the remaining genes [Barbie et al., 2009]. The part that I'm having a hard ...
gsva piano ssgsea egsea written 3 months ago by sina.nassiri50
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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 5 months ago by sina.nassiri50
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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 5 months ago by sina.nassiri50
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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 5 months ago by sina.nassiri50
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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 5 months ago by sina.nassiri50
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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 5 months ago by sina.nassiri50

Latest awards to sina.nassiri

Scholar 5 months 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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