User: ejm32

gravatar for ejm32
ejm32440
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Posts by ejm32

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Differential expression between two biological samples sequenced with single-cel
... You can use any of the standard DEG packages/algorithms (DESeq2, edgeR, limma/voom, etc.), however the question is should you? This [exchange on the Bioconductor support site][1] provides the best rationale for why you should be skeptical/cautious of the analysis you propose. Another option is a mix ...
written 3 months ago by ejm32440
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Comment: C: Tools for Biomarker Signature Generation
... You are welcome. I do not have a sample size recommendation, but a power analysis should be relatively straight forward since you have all the data.... ...
written 12 months ago by ejm32440
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Comment: C: Tools for Biomarker Signature Generation
... The Elastic Net regression is very commonly used for this type of analysis, it combines the strenghs of the Ridge regression and LASSO. Both the CCLE and GDSC papers used the elastic net (though I don't think they shared any code or implementations.) https://www-ncbi-nlm-nih-gov.gate.lib.buffalo.edu ...
written 12 months ago by ejm32440
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Comment: C: Enrichment Analysis in R
... See @Kevin's comment below about meaningfulness of your p-value. But to your direct question, No a p-value of 0 would mean that the overlap is statistically significant. I.e. there is a 0% chance that you would find this degree of overlap or greater if there was no association between the two lists. ...
written 12 months ago by ejm32440
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Comment: C: Enrichment Analysis in R
... You cannot generate per gene p-values for enrichment, only a "set" level enrichment, i.e. does set B overlap with set A more than expected? Maybe you could elaborate on your question/goal? To me, "I would like to check which genes in B are enriched in A", means which genes in B are also in A.... ...
written 12 months ago by ejm32440
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Comment: C: Bioinformatics workshop or training courses
... If you want to do some self-paced learning The Bioconductor workshops provide a good introduction to the Bioconductor ecosystem: https://bioconductor.github.io/BiocWorkshops/ ...
written 12 months ago by ejm32440
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Comment: C: Differential expression analysis of normalized expression of RNA seq data
... This post from the bioconductor support site maybe of help: https://support.bioconductor.org/p/56275/ ...
written 12 months ago by ejm32440
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Comment: C: Interpreting Cliff's Delta Graph
... > Would the 58.93% (Y < X) indicate that the Y group "scored" 58% less than that X group? No, this means that 58.36% Y's are less than the X's. I believe the `d` estimates the probabilityof Y < X which is ~0.4 ...
written 12 months ago by ejm32440
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Comment: C: Mapping Ensembl IDs to Entrez - Merge data frames
... It sounds like you need to perform a `merge` with `genes` and your expression matrix. If the TCGA does not have a version number then you can remove it with `gsub("\\.\\d+","", genes$ensembl_gene_id)` ...
written 12 months ago by ejm32440
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Answer: A: Does microarray cover all genes?
... It does appear that AJUBA is not represented on the Affymetrix Human Genome U133A Array. Furthermore, the code example you provide is incorrect. if you inspect `xx` you'll notice the names of the list elements are the probe IDs, which will always return `NA/NULL`. Here is the code I used to determin ...
written 12 months ago by ejm32440

Latest awards to ejm32

Teacher 10 months ago, created an answer with at least 3 up-votes. For C: How find correlations between ChIP-seq tracks?
Scholar 12 months ago, created an answer that has been accepted. For A: extracting common rows from two files
Voter 17 months ago, voted more than 100 times.
Supporter 2.5 years ago, voted at least 25 times.
Scholar 2.8 years ago, created an answer that has been accepted. For A: extracting common rows from two files

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