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EGSEA gene set testing vooma limma voom gsea

updated 6 months ago by Chris ▴ 20 • written 7.9 years ago by Pekka Kohonen ▴ 190

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Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by daniela.gutierrezandrade • 0

Hello, I am running into a similar issue. After setting the design, at the beginning of the analysis I filter rows with low counts. d…

Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0

Thank you so much for all of your help! I really appreciate it!

Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by Gordon Smyth 51k

Thanks for extra info, but be careful that the Bioconductor support site requires code to be an markdown format. Copying code with prompts …

Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0

Thank you so much for your reply! I am sincerely sorry- of course I do not have multiple GAL files- just one- I meant gpr files! I am so so…

Comment: Is it possible to parallelise saveHDF5SummarizedExperiment by Stefano Mangiola ▴ 20

Thansk Herve', I will try. For reference this is the parallelization implementation of zellkonverter, to save anndata from SCE https://gi…

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Answer: Handling biological replicates in DESeq2

A: Does edgeR need to specify reference group?

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