Hi all,
Is there a way to compute a heatmap before and after applying RUVSeq? I guess in other words, is there a way to apply the RUV factors to the raw counts to generate the heatmap? I'm interesting in the clustering so even just a dendrogram will be sufficient.
Thanks for your help,
M.
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written
by
Michelle M.
See these biostar-posts:
First three are almost your question to some extent, aren't they?
Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
Reorder issue when combining heatmap with dendrogram
Some other posts about heat maps:
What package to use in bioconductor to draw heatmap like this
What Tool To Use To Build An Interactive Heatmap?
Draw Heatmap Or Do Pca Analysis With Raw Read Counts?
Scale Data Before Drawing Heatmap Or Using Heatmap(..., Scale="Columan") In R?
RNAseq heatmap.2 log2FC clustering
Comprehensive guide to heat-maps
https://sumome.com/stories/guide-to-using-heat-maps
Other tools:
https://github.com/TomKellyGenetics/heatmap.2x
https://github.com/jokergoo/ComplexHeatmap
Bioconductor:
Remove Unwanted Variation from RNA-Seq Data
https://www.bioconductor.org/packages/3.3/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf
https://support.bioconductor.org/p/76007/
http://grokbase.com/t/r/bioc-devel/154hp07mkp/bioconductor-3-1-is-released
Thanks Natasha for the comprehensive response, but none of these answer my question. I'm not asking how to make a heatmap. My question was how to apply RUV factors to raw counts before (and after) generating a heatmap.
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