Bioconductor LFC

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1.5k

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deseq2 LFC LRT

written 5.3 years ago by sally.badawi • 0

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811

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GLM prior DESeq LFC

updated 2.0 years ago by Michael Love 42k • written 2.0 years ago by stew • 0

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1.2k

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RNAseq LFC DEseq

3.1 years ago ayy2110 • 0

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1.6k

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deseq2 lfc betaprior

updated 19 months ago by Michael Love 42k • written 5.5 years ago by Mariaxi • 0

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13k

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deseq2 lfc coef contrast

updated 6.9 years ago by Michael Love 42k • written 6.9 years ago by Anke Busch ▴ 10

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2.7k

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limma microarray DEGs p values lfc

7.0 years ago rkp • 0

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18k

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deseq2 deseq lfc lfcse standard error

updated 7.2 years ago by rraadd_8 • 0 • written 7.3 years ago by tootiki • 0

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2.3k

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microarray limma multiple treatments lfc

updated 8.1 years ago by Aaron Lun ★ 28k • written 8.1 years ago by brionyk9 • 0

8 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…

Votes

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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