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Nanostring-Biostats / SpatialDecon

The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
MIT License
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geometric mean of Negprobes #51

Open RM83 opened 1 year ago

RM83 commented 1 year ago

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 commented 1 year ago

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