Bioconductor Downregulated genes

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typo NES rwikipathways downregulated genes gene set enrichment analysis

updated 5.6 years ago by alex.pico ▴ 30 • written 6.0 years ago by Fischer-philipp ▴ 30

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edger differential gene expression upregulated genes downregulated genes

updated 6.6 years ago by lisacarlon25 • 0 • written 6.6 years ago by fawazfebin ▴ 60

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Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0

Hi again, Thank you for the response! Can you expound on why it is not a good idea? I realize that the expression levels/differential expr…

Answer: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k

No, that's not a good idea at all. You should be doing a meta-analysis with these data rather than trying to combine like that. `GeneMeta` …

Answer: GOstats kegg analysis in wheat - help - none of the objects in the first column by James W. MacDonald 67k

Check the help page for `KEGGFrame`. Your columns are out of order.

Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k

You are testing the interaction, so you are asking for those genes that change at any time *differently, depending on the treatment*. If co…

Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0

Thank you both. Special thanks from Prof. Michael Love. It's rare to find tool authors who respond to users so quickly and supportively. Ma…

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Comment: DESeq Input from Salmon + tximport/tximeta

Answer: DESeq Input from Salmon + tximport/tximeta

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