User: SB

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SB0
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Posts by SB

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Comment: C: Interpreting mroast results
... Thanks for your response. Another question has recently come up related to interpreting the mroast results, specifically in understanding the effects of gene weighting. I recently incorporated gene weights into a contrast and compared this result to the same contrast where gene weights were not in ...
written 5 days ago by SB0
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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 each set and sample/comparison along with a p-value and are designed (or at least have proven to perform well) for focused gene set testing with 2 custom gene sets. Further, I'm looking for te ...
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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 8 months ago by SB0
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Comment: C: Interpreting mroast results
... Thank you both for the helpful responses.  ...
written 8 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 8 months ago by SB0
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GSVA: enrichment score bounds and 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 3? Lastly, though I set the scores to be distributed as the difference between the largest positive and negative deviations, the output was not normally distribute ...
gsva written 9 months ago by SB0
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Differential expression of GSVA Enrichment Scores - voomWithQualityWeights and lmfit
... Dear Bioconductors, I am working on using GSVA to look at differential expression of gene set enrichment scores across several sample groups and the dataset I'm using is from NanoString nCounter (which can be treated like RNA-seq count data). I have read that it is recommended to normalize the data ...
limma gsva lmfit voomwithqualityweights written 10 months ago by SB0
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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 3 gene sets in the above samples.​ ...
written 11 months ago by SB0
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GSVA and Limma for differential expression of gene sets
... Dear Bioconductors,   I recently used GSVA to get enrichment scores for three gene sets and four sample groups. From the enrichment scores, I am interested in determining if they are differentially expressed across several sample groups. I intend to do many sets of comparisons and thus I was planni ...
limma gsva written 11 months ago by SB0
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GSVA with NanoString nCounter data
... 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 ...
gsva nanostring written 13 months ago by SB0

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Supporter 8 months ago, voted at least 25 times.

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