geometric mean of Negprobes

[RM83]

I received raw counts and normalized GeoMX data. The raw counts data contain multiple negative probes (negprobe-WTX). Do I need to compute the geometric mean of these negative probes in the raw counts data before using it in SpatialDecon? If so, please confirm whether I should calculate the geometric mean per column. Alternatively, may I exclude the negative probes from the raw counts and exclude the negprobe-WTX from the normalized data after computing per.observation.mean.neg and background matrix bg using the normalized data?

[maddygriz]

Hi @RM83 ,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks,
Maddy