Bioconductor Read.maimages

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limma read.maimages normalization preprocessing

updated 6.8 years ago by Gordon Smyth 51k • written 6.8 years ago by marviedemit ▴ 10

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limma read.maimages

updated 7.0 years ago by Gordon Smyth 51k • written 17.9 years ago by Lakshmanan Iyer ▴ 250

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differential gene expression limma read.maimages

updated 9.4 years ago by Gordon Smyth 51k • written 9.4 years ago by SSK ▴ 10

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limma bioconductor read.maimages agilent 8x60K

9.6 years ago wd ▴ 30

4 results • Page 1 of 1

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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 …

Comment: Are transformed values from rlog /vst log2 normalized counts? by James W. MacDonald 67k

The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …

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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

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Scholar to James W. MacDonald 67k