I'm using Deseq2 analysis and I have 52 samples and on the stage of prefiltering I'm not sure if I have to use:
keep <- rowSums(counts(dds)) >= patients_number
dds2 <- dds[keep,]
dds2
or
keep <- rowSums(counts(dds)) >= patients_number/2
dds2 <- dds[keep,]
dds2
My original dimensions of my samples were:
class: DESeqDataSet
dim: 62758 52
metadata(1): version
assays(1): counts
rownames(62758): ENSG00000000005 ENSG00000000419 ... __not_aligned __alignment_not_unique
rowData names(0):
colnames(52): V3 V32 ... V80PLUS9 VRM6
colData names(2): Groups Newgroup
And after trying both patients_number or patients_number/2 the results were respectively:
dim: 19202 52 and dim: 21984 52
But I don't know which to keep.