Bioconductor ReactomeGSA

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BiologicalQuestion ReactomeGSA BatchEffect

updated 10 days ago by jg ▴ 20 • written 13 days ago by Shaimaa Gamal • 0

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ReactomeGSA BatchEffect RNASeqData

updated 10 days ago by jg ▴ 20 • written 4 months ago by Shaimaa Gamal • 0

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Answer: Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value by Michael Love 42k

This is covered in the workflow (rnaseqGene). You can filter them, but no they will not negatively affect the multiple testing because o…

Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10

Thank you, the strange thing is that I am only getting positive effect sizes. I [see two relevant definitions][1]: - Eff_* : The effect s…

Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k

The odds ratio, not log FC. My bad.

Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k

``` testResult$Eff_Condition > 0.1 ```

Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0

I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…

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Answer: object 'hdac_targets' not found

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