Biostar Ashr

Showing : ashr • reset

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ashr DESeq2 lfcShrink svalue

4 months ago Enrico • 0

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178

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deseq2 ashr

10 months ago da.de ▴ 20

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366

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deseq2 ashr rna-seq

15 months ago Alex • 0

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128

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ashr

15 months ago kavator ▴ 20

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176

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ashr Deseq2 lfcThreshold

updated 15 months ago by Michael Love 33k • written 15 months ago by Iryna • 0

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Answer: Wrong stdev.unscaled from contrasts.fit when lmFit contains a weights matrix by Gordon Smyth 43k

First, the design matrix and contrast you have created are extremely artificial and I cannot see how they could be used for any real analys…

Answer: Help With TCGAbiolinks package by Kevin Blighe 3.2k

Hi Daniela, The raw counts should be contained in the `HGNC.exp` object under the '`raw_count`' assay: HNSC.exp class: RangedSum…

Comment: Problems with installation of 'phyloseq by Kevin Blighe 3.2k

Great, thanks for the feedback, Ina

Comment: featureCounts - paired-end data by Wei Shi ★ 3.3k

You need to specify `-p` and `--countReadPairs` to count fragments instead of reads. The value provided to the `-t` option is typically `ex…

Comment: Problems with installation of 'phyloseq by Ina • 0

Hello, I used the code to install 'GenomeInfoDbData' from Bioconductor- which worked. Then I tried to install 'phyloseq' from Bioconductor…

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Comment: derfinder model.matrix with limma or single base-level F-statistics analysis

Answer: derfinder model.matrix with limma or single base-level F-statistics analysis

A: DESeq2: multiple conditions design -- How to select subset comparisons from the

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