Bioconductor Vanillaice

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1.6k

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Annotation Cancer Breast VanillaICE copynumber Annotation Cancer Breast VanillaICE

15.9 years ago Steven McKinney ▴ 310

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1.5k

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SNP6 crlmm vanillaice vanillaice crlmm cnv

updated 9.4 years ago by rscharpf • 0 • written 9.4 years ago by cafelumiere12 ▴ 20

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1.3k

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Proteomics VanillaICE Proteomics VanillaICE

updated 12.9 years ago by Valerie Obenchain ★ 6.8k • written 12.9 years ago by Francesco Mancuso ▴ 110

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1.2k

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crlmm vanillaice

9.3 years ago Shi, Tao ▴ 720

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Annotation Cancer VanillaICE crlmm Annotation Cancer VanillaICE crlmm

13.0 years ago Daniel Rico ▴ 110

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SNP Cancer graph oligo SNPchip oligoClasses VanillaICE crlmm SNP Cancer graph oligo

15.4 years ago Min-Han Tan ▴ 40

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SNP affy VanillaICE SNP affy VanillaICE

12.6 years ago Rob Scharpf ▴ 250

7 results • Page 1 of 1

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Answer: How to subset voomLmFit (MArrayLM) object? by Gordon Smyth 51k

Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…

Answer: Need help interpreting heatmaps from limma by James W. MacDonald 67k

Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …

Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10

I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…

Answer: featureCounts fails to load annotation file by James W. MacDonald 67k

I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…

Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k

That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …

Votes

Answer: Are transformed values from rlog /vst log2 normalized counts?

Comment: Are transformed values from rlog /vst log2 normalized counts?

Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable

Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical

Awards • All

Scholar to James W. MacDonald 67k