Bioconductor PAPi

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PAPi metabolomics pathway analysis raphael

6.3 years ago maryke.wijma • 0

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papi metabolomics pathway analysis

updated 7.7 years ago by k_hulce ▴ 10 • written 8.6 years ago by hp71727 ▴ 10

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PAPi

7.8 years ago k_hulce ▴ 10

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Pathways PAPi Pathways PAPi

updated 10.9 years ago by Aggio, Raphael ▴ 20 • written 10.9 years ago by Guest User ★ 13k

4 results • Page 1 of 1

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Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k

I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…

Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0

Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…

Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k

I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Fahd • 0

Thanks for looking into this. This issue results in the incorrect usage of multiple ORA software including EnrichR.

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k

Yes, I understand the implications of replacing the `OrgDb` packages in release. Maybe an upload to the annotationHub or GitHub could be an…

Votes

A: p.adjust BH generates duplicate values

Answer: Adjusted p-values become NA when sub-setting samples

Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice

Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim

A: How does edgeR cpm function calculate log(CPM) values?

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