Determining if a published count matrix was already corrected by SCTransform #8372
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adam-cornwell
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Hi, I am trying to work with a published dataset, for which the sparse matrices were provided in GEO (GSE223972), but no data was uploaded to SRA. It appears that it's not the count matrix from CellRanger, because it seems like cells with a high fraction of mito-associated reads were already filtered out. The publication says they used SCTransform, but there is no information in GEO as to if the counts they uploaded were original counts, or SCT "corrected" counts. It would be easy to tell if they were SCT post-log-transform, which they are not.
Is there a way to tell if counts are the non-log-transformed SCT "corrected" counts or "raw" counts? I do not want to end up running SCTransform on data that was already normalized.
I did not see answers to this particular question that exist, though of course if I missed it please let me know.
Thanks!
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