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I noticed that Alra doesn't use the scaled data for it's imputation. Is this by design?
I'm not using the default SCTransform function to normalize my data but the 'old' NormalizeData %>% FindVariableFeatures %>% ScaleData pipeline. I noticed that I get the same result from Alra regardless of whether I perform the ScaleData step.
It seems Alra is using the data values and not the values stored in scaled.data. If this is by design, I guess I need to run ScaleData after Alra to obtain scaled expression values? If this is the case, it seems a bit misleading to me that one would think the data is scaled/centered when it isn't after Alra has run.
The text was updated successfully, but these errors were encountered:
I noticed that Alra doesn't use the scaled data for it's imputation. Is this by design?
I'm not using the default SCTransform function to normalize my data but the 'old' NormalizeData %>% FindVariableFeatures %>% ScaleData pipeline. I noticed that I get the same result from Alra regardless of whether I perform the ScaleData step.
code to reproduce:
It seems Alra is using the
data
values and not the values stored inscaled.data
. If this is by design, I guess I need to run ScaleData after Alra to obtain scaled expression values? If this is the case, it seems a bit misleading to me that one would think the data is scaled/centered when it isn't after Alra has run.The text was updated successfully, but these errors were encountered: