Sample annotation for cemitool

Question

[Expert]

There is a sample_annot function in cemitool package. I don't have an idea for sample annotation. My Sample barcode is TCGA... how is sample annotation for cell line or time point in R? Do you know this?

Answer 1

[pedrostrusso]

Sample annotation isn't required in CEMiTool. If you have no idea for what to use, you can just skip using it altogether, and just use the cemitool function as follows:

cem <- cemitool(expr)

where expr is your expression data with genes in the rows, samples in the columns, and gene names in the rownames.

Hope this helps,

Pedro

[Kind Katydid]

Original message deleted - turns out I had a buggy R session where nothing plotted. it's all good :)