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EdgeR normalization fastq txt TMM

updated 2.8 years ago by Gordon Smyth 52k • written 9.3 years ago by hamidrezarazzaghian • 0

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Affymetrix CEL TXT

updated 5.2 years ago by James W. MacDonald 68k • written 5.2 years ago by pbachali ▴ 50

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read.table TXT

updated 5.3 years ago by James W. MacDonald 68k • written 5.3 years ago by ekl • 0

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Annotation GEO TXT

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Files TXT

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qPCRset object nondetects r package txt

updated 16 months ago by Nat.Nataren • 0 • written 7.1 years ago by s.m.may • 0

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r TXT codelink

9.6 years ago Agaz Hussain Wani ▴ 260

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Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k

> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…

Answer: Automatically install dependencies by ATpoint ★ 4.7k

The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…

Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k

> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…

Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k

This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…

Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k

Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…

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A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo

Comment: Weird p-values using DESeq2?

Comment: Overcoming confounding in batch effect correction

Answer: Store Matrix in DataFrame Cell

Answer: enrichGOgradient color change

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