Single Cell RNA seq imputation with MAGIC – scale of output?
I ran MAGIC on some single cell seq data and am curious of the scale of the output? I first used Seurat’s normalization function which converts the raw counts to CPM and then natural log transforms the data. After applying MAGIC is the data on a linear scale or natural log scale?
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What does it look like when you plot the distribution of values?
Based on the comments of the author here, I assume that the scale of the values should not have changed (there should just be a lot fewer zeros), BUT there may be small negative values because “after MAGIC the imputed data (imputed PCs) are projected back to the original space and as a result there can be (very small) negative values” github issue.
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