"Samples in group not continuous" when trying to upload counts matrix

[skudashev]

Hello,

I am trying to use a counts matrix generated with Salmon. I have not used any scaling normalisation when creating the matrix:
cts <- tximport(files, countsFromAbundance = "no", type = "salmon", tx2gene=tx2gene[,c("transcript_id", "gene_id")] counts <- cts$counts
However, when I try generating a new project in tappas, I get an error message saying that the matrix must contain raw counts.

Could you please help me understand what I can do to make this data suitable for tappas?

Kind regards,

Sofia

[aarzalluz]

Hi @kudasonya.

This is probably not the source of the error, since tappAS can handle double values as counts for analysis (I've used it with the abundances output by RSEM, which are not integer).

Could you print a snapshot of what your expression matrix looks like? Perhaps there is other formatting error happening.

Best,

Ángeles