I am approaching the analysis of single-cell RNA-seq data.
I have seen that Seurat package offers the option in
FindMarkers (or also with the function
DESeq2DETest) to use DESeq2 to analyze differential expression in two group of cells.
Assuming I have group A containing n_A cells and group_B containing n_B cells, is the result of the analysis identical to running DESeq2 on raw counts of each gene in n_A versus n_B samples? And is there a way to speed up the analysis when n_A and n_B are in the order if a few thousands cells?
In addition, I have a 'technical' question:
when I have a count table in the form of a data.frame (for example read with read.table from a text file), is it necessary to force it to matrix such as
cts <- as.matrix(cts) before providing it as input to
DESeqDataSetFromMatrix? It seems to be I can just provide the count table as a data frame.