User: atakanekiz

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atakanekiz20
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2 months, 4 weeks ago
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Posts by atakanekiz

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Significant but very small beta coefficients in Cox proportional hazards calcula
... Sorry my bad. Thanks for the directions. ...
written 4 months ago by atakanekiz20
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Comment: C: Significant but very small beta coefficients in Cox proportional hazards calcula
... Thanks for your reply. I thought this could be related to the functions of "survival" package, that's why I posted here. I posted in CV and Biostars just now as well. Hopefully will hear something back. ...
written 4 months ago by atakanekiz20
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(Closed) Significant but very small beta coefficients in Cox proportional hazards calculation
... Hello BC community, I'm analyzing TCGA data to investigate the effects of lncRNAs on survival. Among other things, I wanted to calculate a univariate CoxPH model for each gene to find genes whose expression levels have a significant correlation with survival outcome. I realize that I'm not testing ...
survival survival analysis cox hazard ratio coxph written 4 months ago by atakanekiz20
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Comment: C: Understanding clusterprofiler enrichment results
... Thanks for your message, but I'm not sure if it resolves my question. I can visualize the results as a data frame or in the form of a graph, but the results inherently don't show which gene sets are enriched in one vs the other phenotype. What I'm looking for is something equivalent to positive and ...
written 4 months ago by atakanekiz20
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Comment: C: fgsea p-values are mostly the same upon analysis
... Sorry, it took me a while to respond. I'm attaching a csv file with the gene ranking. I don't think it is the same as the initial analysis I posted in this thread, but the same issue persists here as well.  https://nofile.io/f/3Skt1b8xqZ1/neutrophil_ranked_genes.csv ...
written 4 months ago by atakanekiz20
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Comment: A: fgsea p-values are mostly the same upon analysis
... I think might have an idea... The sc-rnaseq data type doesn't really feature a high dynamic range of measurements. Unlike counts obtained from a bulk RNAseq, individual cells often register a few copies of a transcript. Therefore, it isn't uncommon to find expression values of 1-3 per gene per cell. ...
written 4 months ago by atakanekiz20
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fgsea p-values are mostly the same upon analysis
... Hello,   I'm analyzing enrichment scores of MSigDB gene list in the subsets of my single cell rnaseq data. I'm using S2N metric implemented in GSEA (I just wrote a function to perform this for me and feed it into fgsea). I got everything to work but I'm trying to ensure what I see is actually real ...
gsea fgsea sc-rnaseq written 4 months ago by atakanekiz20
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Answer: A: pre-ranked GSEA within R: options?
... I've been playing with GSEA analyses in the last couple of days by using my single cell rnaseq data. I automated sample subsetting, gene ranking (S2N method, but can be replaced by other metrics), performing GSEA (using fgsea package) and reporting the top hits. If you are still interested in this t ...
written 4 months ago by atakanekiz20
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Understanding clusterprofiler enrichment results
... Dear BC community,   I have performed gene set enrichment analysis by using clusterprofiler package. I prepared a gene list by using package vignettes and got everything working, but I'm having a bit of a hard time interpreting the results. I read pretty much all the questions and the vignettes ab ...
clusterprofiler sc-rnaseq gene set enrichment analysis enricher written 4 months ago by atakanekiz20 • updated 4 months ago by Guangchuang Yu1.1k
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Answer: A: GAGE analysis with the whole or a subset of matrix
... I actually figured out the problem. There was a mistake in my code while resulting in erroneous output. I can now confirm that regardless of the input matrix size, as long as the column annotations (ie `ref` vs `samp` are done properly, GAGE gives the same output. Hopefully, this might help somebody ...
written 4 months ago by atakanekiz20

Latest awards to atakanekiz

Scholar 6 months ago, created an answer that has been accepted. For A: Differences between RTCGA and TCGAbiolinks data
Scholar 6 months ago, created an answer that has been accepted. For A: GAGE analysis with the whole or a subset of matrix

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