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genetics GeneticsPed Genetics

23 months ago Gülsüm • 0

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Sequencing Genetics GeneticsPed statistics

4.8 years ago António Miguel de Jesus Domingues ▴ 510

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Genetics GeneticsPed Genetics GeneticsPed

updated 12.3 years ago by Dan Tenenbaum ★ 8.2k • written 12.3 years ago by Liz Hare ▴ 30

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Genetics GeneticsPed Genetics GeneticsPed

updated 17.0 years ago by Vincent J. Carey, Jr. 6.7k • written 17.0 years ago by Paolo Innocenti ▴ 320

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Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

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Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

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