User: SB

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SB0
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Posts by SB

<prev • 9 results • page 1 of 1 • next >
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Focused gene set tests
... Dear Bioconductor community, I'm looking for gene set analysis tests that produce a quantitative value for either each set and/or each sample along with a p-value and are designed (or at least have proven to perform well) for focused gene set testing with only 2 sets. Further, I'm looking for a tes ...
gene set analysis gene set testing gene set enrichment analysis written 3 months ago by SB0 • updated 3 months ago by Gordon Smyth36k
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Comment: C: GSVA: enrichment score bounds and enrichment score transformations
... Thank you for the response. If I have a data set with a total of 16 samples (4 per treatment group) then would you say that the non-parametric density estimation would not produce reliable results? I was confused in the article as to whether sample means "observations" (i.e. samples per treatment gr ...
written 3 months ago by SB0
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Comment: C: Interpreting mroast results
... Thank you both for the helpful responses.  ...
written 3 months ago by SB0
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Interpreting mroast results
... Dear Bioconductor community, In a couple of my comparisons using the mroast gene set test I received some confusing results (as shown below). Notably, I understand that there are no significantly differentially expressed genes in either (up or down) or both directions (both prior to and following B ...
limma roast mroast written 3 months ago by SB0
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GSVA: enrichment score bounds and enrichment score transformations
... Dear Bioconductors,  It looks like the GSVA enrichment scores are bound between -1 and 1. Is this true? If so, is this ensured in step 2, when the expression-level statistics are converted to ranks and normalized to make the ranks symmetric around zero and/or step 3? Lastly, though I set the score ...
gsva written 4 months ago by SB0 • updated 4 months ago by Robert Castelo2.3k
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Differential Expression of GSVA Enrichment Scores - pre-processing with voomWithQualityWeights and GSVA follow-up with lmfit
... Dear Bioconductors, I am working on using GSVA and determining differential expression of gene set enrichment scores across different phenotypes of a certain immune cell. The dataset I'm using is from NanoString nCounter (which can be treated like RNA-seq count data) and my first question is in reg ...
limma gsva lmfit voomwithqualityweights written 5 months ago by SB0 • updated 5 months ago by Robert Castelo2.3k
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Comment: C: GSVA & Limma for DE of Gene Sets using NanoString Data
... Yes, three rows since I am only interested in examining enrichment of three gene sets (M1, M2a, and M2c) in the above samples.​ ...
written 6 months ago by SB0
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GSVA & Limma for DE of Gene Sets using NanoString Data
... Dear Bioconductors,   I recently used GSVA to get enrichment scores for 3 pathways (i.e. gene sets) using an expression matrix that was generated with NanoString nCounter. Prior to using the expression matrix with GSVA, the data was normalized according to the NanoString manual and log2 transformed ...
limma gsva limma design matrix nanostring limma contrast matrix written 6 months ago by SB0 • updated 6 months ago by Robert Castelo2.3k
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GSVA with NanoString nCounter Data - Pre-Processing
... Dear Bioconductors,  I am quite new to bioinformatics analysis and am interested in using the GSVA function with NanoString nCounter Data. I have read that "the NanoString nCounter is most similar to RNA-Seq in that it processes discrete counts of measurement similar to RNA-Seq." Thus, I was under ...
preprocessing gsva nanostring written 8 months ago by SB0 • updated 8 months ago by Robert Castelo2.3k

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