My sample annotation file has names with A001, A002, ..., B001, B002, ..., C001, ..... but rnbeads output file shows names with X1, X2, ..., X433.

Why does this difference occur? Is this a reliable result? Can I just think of it as being printed in the order I entered it?

My codes are below:

> idat.dir<-"/directory/idat_all"
> sample.annotation <- "/directory/sample_sheet_1678.csv"
> analysis.dir <-"/directory/rnbeads5_2"
>
> rnb.options(filtering.snp = "3",
+           filtering.sex.chromosomes.removal = TRUE,
+             filtering.cross.reactive = TRUE,
+             filtering.greedycut.pvalue.threshold = 0.01,
+             identifiers.column = "name",
+             normalization.method = "bmiq",
+             export.to.csv = TRUE,
+             exploratory = FALSE,
+             differential = FALSE)

> library(grid)
> rnb.run.analysis(dir.reports = analysis.dir, sample.sheet = sample.annotation,
+                  data.dir = idat.dir, data.type = "idat.dir")