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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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median filtering and clustering by groups #441

Open msherafatian opened 2 years ago

msherafatian commented 2 years ago

Hi Thank you for helping us resolve the issues and interpret the results. I was wondering why I get different levels of filtering when I apply the median filtering with or without cluster_by_groups? When I use my previously defined clusters I get a better filtering of the noise and a much cleaner result.

cluster_by_groups = T image

cluster_by_groups = F

image

GeorgescuC commented 2 years ago

Hi @msherafatian ,

Which version of infercnv are you running, and what are the other options you are using? More specifically, the options related to clustering and analysis mode.

Are you changing the cluster_by_groups option when running the whole analysis, or only when plotting? The median filtering uses the clustering information stored in the object, so if you change the option in the plotting only, it might have to recalculate the hierarchical clustering on different groups and sorting of cells than the filtering was applied on.

Regards, Christophe.