Bioconductor Microarrays

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2.4k

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limma sample size microarrays statistical power

6.5 years ago eleonoregravier ▴ 70

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microarrays xml RCurl libxml2 libcurl

updated 7.5 years ago by Martin Morgan 25k • written 7.5 years ago by farahqureshi5 • 0

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875

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whole human genome microarray 4x44k microarrays

7.5 years ago farahqureshi5 • 0

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limma cmap microarrays differential gene expression

7.6 years ago kevin.m.hao ▴ 10

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limma design matrix limma limma contrast matrix microarrays

8.2 years ago miyuki_iii ▴ 10

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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…

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

I use `minfi` for preprocessing and `DMRcate` for DMR. I like `preprocessFunnorm` (and possibly the XY-interpolated version in the `wateRme…

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

I gave you busted SQL code that returned the central key for the DB rather than the gene IDs. Here's the corrected version. ``` > mgis <- …

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

Thank you very much. What package do you use/recommend? (I see there are several options, so I went with sesame but I don't have to use tha…

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

Oh, ok. For background, I don't use `sesame`, so this is new territory for me as well. I see why the effect size is always positive thoug…

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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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