Heatmap before and after RUVSeq

Question

[Michelle M.]

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.

Answer 1

[natasha.sernova]

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:

http://rpkg.gepuro.net/

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

https://github.com/Bioconductor-mirror/RUVSeq

[Michelle M.]

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.

[whxqmy]

Hi Michelle! It has been a long time since you asked the questions. I am running into the same problem and wondering if you have figured out the way to plot a heatmap after ruvseq correction. Thanks!

[luca]

Hi everyone. I have the same "problem"/question. It would be interesting to know how to do what Michelle has asked. Thanks a lot!

[thyleal]

I know it's late, but if anyone needs in future: you can use limma::removeBatchEffect() function from limma R package on your normalized log counts (you can use edgeR::cpm() for this using the log = TRUE). Please read those functions documentations.