Bioconductor Shrinkage

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shrinkage DifferentialExpression DESeq2

updated 19 months ago by ATpoint ★ 4.7k • written 19 months ago by Abir.khazaal ▴ 10

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1.2k

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shrinkage apeglm

2.9 years ago Frederik Ziebell ▴ 30

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3.0k

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deseq2 shrinkage

updated 2.3 years ago by Michael Love 43k • written 5.0 years ago by Nicolas Rosewick ▴ 20

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1.4k

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deseq2 shrinkage

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by vvi • 0

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4.6k

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deseq2 betaPrior shrinkage significance

6.8 years ago brynedal ▴ 40

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1.6k

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deseq2 log2fc shrinkage

updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by aec ▴ 90

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Answer: Differential expression of proteins using somascan data by James W. MacDonald 68k

Providing a bunch of code but not the output is not very helpful. Ideally you would just provide ``` nrow(design) ncol(protein_data_lo…

Comment: Surprising behavior for DEXseq dispersion estimate plot? by Elijah • 0

Hi Snow, Thanks for your comment! I didn't do any normalization of the counts prior to the DEXseq pipeline - I've only been using the inte…

Comment: Using tximport for kallisto aligned TOIL data by Nicholas • 0

Sorry, I misspoke. The data was from the TOIL project and was aligned using kallisto. It was accessed from the UCSC XENA browser. I updated…

Comment: Using tximport for kallisto aligned recount2 data by ATpoint ★ 4.7k

recount 2 does not use kallisto, does it? And recount does offer genelevel counts, so what's the point?

Comment: Seeking Advice on HTA 2.0 Microarray Data Processing with Oligo Package by Yao Lipu • 0

Thank you for your help! Your explanation was very clear and really helped me solve my issue. I truly appreciate your time and effort!

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Answer: Differential expression of proteins using somascan data

Answer: Surprising behavior for DEXseq dispersion estimate plot?

Answer: Handle zero effective gene length when tximport RSEM results

Handle zero effective gene length when tximport RSEM results

How to remove genes with 0 counts in tximport?

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