Bioconductor Quality

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RNA-seq PCA control DESeq2 Quality

2.6 years ago • updated 2.4 years ago 9906201a ▴ 20

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microarray quality

updated 5.6 years ago by Wolfgang Huber ★ 13k • written 5.7 years ago by RV ▴ 10

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folder quality QualityControl AffyExpress

3.8 years ago bastien_chassagnol • 0

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base quality quality mean base quality

updated 7.9 years ago by Mike Smith ★ 6.5k • written 7.9 years ago by christiangriffioen • 0

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Comment: How to use removeBatchEffect for removing effect of multiple confounding variabl by James W. MacDonald 67k

Please don't add questions onto a four-year old post. Instead, start a new one. If you want to reference the old post, that's fine.

Answer: How to use removeBatchEffect for removing effect of multiple confounding variabl by bioinformata • 0

Is it feasible to remove batch effect with limma after variance stabilizing transformation of the gene expression , or is eough to use vst…

Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k

Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …

Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20

Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…

Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Guido Hooiveld ★ 4.1k

Hi James, I am likely missing something obvious, but why is the code that I used returning a different number of genes having a GOALL-BP a…

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Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th

Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus

Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th

Answer: object 'hdac_targets' not found

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