Normalized expression values in Data Table?

[Prisca]

Hello,

I am examining the "Data Table" tab within the "DataView" module and noticed that the gene expression values in the table have decimals while the original gene count matrix I supplied consisted only of integers. Can someone clarify if/how the data is normalized or adjusted to obtain the values observed? I currently have the settings set to "ungrouped" (no averaging) and "linear" (instead of "log2"). I check the documentation regarding this tab and I think it is outdated.

Thank you,

Prisca

[Ivo Kwee]

Hi Prisca. You are right. That data is linear but normalized (depending on the normalization you choose, likely CPM+quantile). It is normalized because it would not make sense to compare (linear) intensities between samples with unnormalized counts. I agree that it might be useful to see the actual counts to check your data. Perhaps we can add in future raw unnormalized data there just for checking raw counts.  Best. Ivo.

[pio28]

Thanks Ivo! This information is just what I was looking for.