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bug graper offtopic

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RNA-Seq sequencer library_size sequency_depth multiplexing offtopic

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mygene offtopic

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ChIPSeq SICER2 DiffBind MACS2 offtopic

updated 3.9 years ago by James W. MacDonald 68k • written 3.9 years ago by Yuan Tian ▴ 290

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Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0

Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…

Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0

Thank you so much for your reply.

Comment: Analyzing TnSeq data with DESeq2 by Tom • 0

[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…

Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k

This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…

Comment: Filtering after DESeq by caroline.zanchi • 0

... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…

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A: DESeq2::sizeFactors() function does not output the sizeFactor table.

Comment: Filtering after DESeq

A: Normalized counts from DESeq2 results in similar but not equal total read count?

A: DESeq2: Different Dispersions for different sample groups

A: Contrasts & coefficients in limma

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Great Question to inzirio ▴ 10