Bioconductor SpikeIn

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SpikeIn DESeq2 Normalization

written 8 months ago by ADopico • 0

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DESeq2 SpikeIn Normalization

updated 11 months ago by maria.soler • 0 • written 2.2 years ago by kalavattam ▴ 10

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SpikeIn RUVSeq DESeq2 RUV

updated 9 months ago by Michael Love 43k • written 9 months ago by Ειρήνη • 0

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sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn

updated 5 months ago by ATpoint ★ 4.8k • written 5 months ago by Katerina • 0

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Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k

I dove a bit deeper to understand more the differences between `scuttle::logNormCounts()` and `edgeR::cpm(log = TRUE)` at https://github.co…

Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k

Thanks for the answer James! I had forgotten about the "PM" part of CPM when I met with Kinnary yesterday!

Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k

Thank you Gordon for the detailed answer, examples, and link to the unpublished thesis!

Answer: Make DEXSeq plot normal scale by James W. MacDonald 68k

It's hard coded, so you will not be able to change the vertical axis of the top plot without getting the code and modifying. You can simply…

Answer: RNA Seq using Lrt by James W. MacDonald 68k

When you perform an LRT, you are testing the coefficients that are no longer included in the reduced model. So you are testing to see if in…

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Comment: edgeR::cpm() results in negative values from raw counts of 0

Answer: edgeR::cpm() results in negative values from raw counts of 0

edgeR::cpm() results in negative values from raw counts of 0

Answer: edgeR::cpm() results in negative values from raw counts of 0

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