Make heatmap for RCC files in Rstudio(NanoStringNorm)

Question

[cseplomarton]

Hi everyone!

I want to create a heatmap for my RCC(not xls format) files in Rstudio. The problem is that the usual tools like heatmap.2 or heatmaply can't take the dataset of RCC files as a valid argument. The make.count.heatmap() also not woks. Can anyone help with that?

Answer 1

[Kevin Blighe]

You can use nSolver (free) for Windows, if you want.

Otherwise, you can import the RCC files as raw counts into R on any platform via NanoStringQCPro and then conduct normalisation and differential expression via DESeq2, followed by heatmaps, of course. For normalisation, you may want to use RUVSeq with the NanoString's housekeepers. There is a vignette for how to do this, I believe - please search.

You can also conduct normalisation via NanoStringQCPro on its own to produce log [base 2] normalised expression levels, and then employ your own tests on these.

Kevin