Can I still remove ambient RNA if I do not have raw barcode-gene matrix?

Question

[malonzm1]

Hi,

I would like to use SoupX for ambient RNA removal. However, I am using barcode-gene matrix datasets downloaded from NCBI GEO which don't always include raw data. Can I still use SoupX without the raw barcode-gene matrix?

Thanks and good day.

[bk11]

No, it will not work without raw counts (tod). SoupX requires requires table of counts (toc) and pass that along with the raw counts (tod) to create SoupChannel which will be used to estimate what the expression profile of the soup.

[malonzm1]

Many thanks.