Bioconductor Des

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 7 weeks ago by James W. MacDonald 66k • written 7 weeks ago by Alexandre • 0

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169

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Des DESeq2

updated 9 weeks ago by hemantcnaik • 0 • written 9 weeks ago by Sahar • 0

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DESeq2 DEs

3 months ago feather-W • 0

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540

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DESeq2 des

updated 18 months ago by Michael Love 42k • written 19 months ago by Devin • 0

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594

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DES DESIGN

updated 21 months ago by Michael Love 42k • written 21 months ago by mike • 0

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650

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DESeq2 DES

updated 3.5 years ago by Michael Love 42k • written 3.5 years ago by heikki.sarin ▴ 10

6 results • Page 1 of 1

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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100

Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz

Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k

The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …

Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k

You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.

Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0

In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…

Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k

For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…

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Comment: Most enriched pathway is not expressed when modifying universe parameter

Time-course, comparison of two groups

Answer: Behaviour of featureCounts when quantifying multi-mapping reads

Answer: GESA with certain gene list returns no result with human genom, but many result

Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`

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