Is NormalizeData(LogNormalize) not generating RPM values?

[dmoaks]

I was hoping to ask about the exact calculation happening in NormalizeData under the LogNormalize option, as it is not explicitly stated in the documentation. I’m trying to obtain RPM/TPM values for the data table, but this function seems to be dividing every cell by the same number rather than a cell-specific scaling factor. What does the “scale factor” variable do in NormalizeData? How do I normalize to the expression of the individual cell?

[thbin]

The following CPP codes are the implementation for the LogNormalize.
The normalize algorithm is log1p(value/colSums[cell-idx] *scale_factor), and colSums[cell-idx] is total expression value for each cell.

Eigen::SparseMatrix<double> LogNorm(Eigen::SparseMatrix<double> data, int scale_factor, bool display_progress = true){
  Progress p(data.outerSize(), display_progress);
  Eigen::VectorXd colSums = data.transpose() * Eigen::VectorXd::Ones(data.cols());
  for (int k=0; k < data.outerSize(); ++k){
    p.increment();
    for (Eigen::SparseMatrix<double>::InnerIterator it(data, k); it; ++it){
      data.coeffRef(it.row(), it.col()) = log1p(double(it.value()) / colSums[k] * scale_factor);
    }
  }
  return data;
}

[jcamunas]

I was also facing a similar doubt with LogNormalize. I understand from this answer that you are actually using the natural logarithm (not log10 or log2) when doing log1p. Could you confirm this point? Thanks!

[leonfodoulian]

@jcamunas : log1p(x) is equivalent to log(x + 1).

Best,
Leon

[iiiir]

This might be a naive question: why the log transformed matrix, still having median/mean ~1700 (UMIs), compared to before normalization median of ~2200.
I am referring to the PBMC 2700 dataset, the @DaTa slot of teh seurat objects.

[jon-xu]

@iiiir the unit of measure has been different.