Hello, I am working with 10x Genomics scRNA-seq data. I am using
Seurat::CellCycleScoring() to assign cell cycle stages to cells and
batchelor::regressBatches() to remove this unwanted source of variation.
My question is regarding output from regressBatches().
As documentation says, the output is "A SingleCellExperiment object containing the corrected assay.",
where corrected assay is object of class ResidualMatrix,
and "the residuals represent the expression values after correcting for the batch effect".
I am really not sure if I am using the ResidualMatrix properly in downstream analyses.
I have used this matrix to calculate dimreds, clustering and to find cluster markers.
Although I can see that some genes are relatively good markers (log2FC > 1, FDR < 0.1;
Seurat::FindAllMarkers() using Wilcox test),
the heatmap of such genes is not very convincing (see below - top 15 upregulated genes from each cluster).
For example, the first gene (IGFBP5) has log2FC of 2.2 in the first cluster, but I can barely see a difference in the heatmap.
I am not sure if this is just caused by improper color gradient, but you can see that are negative values in the ResidualMatrix.
Thanks in advance for reply!