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KChen-lab / SCMarker

Marker gene selection from scRNA-seq data

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Input expression data: log or anti-log?

randel opened this issue · comments

commented

When using this nice package, I was confused by whether the input expression should be log or anti-log transformed.

The example data are log-transfromed.

data(melanoma)
melanoma1 = as.matrix(melanoma[, 2:dim(melanoma)[2]])
row.names(melanoma1) = melanoma[, 1]
range(melanoma1)
[1]  0.000 15.923

In SCcluster(), NormalizeData() from the Seurat is called, and data are log-transformed again by normalization.method = "LogNormalize".

Then in getClusterGene(), get_marker_genes() from the SC3 package is called. According to its example, get_marker_genes() takes in anti-log transformed data as input, other than the log-transformed data.

range(yan[1:10,])
[1]    0 9225
commented

SCmarker can select markers from either raw expression data or log transformed. It does not require any normalization. If you want to integrate SCMarker to other tools (Seurat or SC3), anti-log transformed would be recommended.