I am trying to look at a relatively old mouse data that was taken using Expression Chip v6.1.1. The problem came I when I tried to convert Probe IDs to gene names. Probe IDs are, for example: 10243, 10280, 10575, 20048, ..., 102900072, 102900075, ...
I tried an old keys/mapIds way using 3 packages: illuminaMousev1.db, illuminaMousev1.1.db, illuminaMousev2.db and none had Probe IDs similar to what I got from GEO file
As an example of how I did it:
toget <- c("GENENAME","SYMBOL","ENTREZID","ENSEMBL", "ACCNUM") library("illuminaMousev1.db") ks <- keys(illuminaMousev1.db) annData1 <- as.data.frame(lapply(toget, function(x) mapIds(illuminaMousev1.db, ks, x, "PROBEID")))
I eventually (possibly) succeeded using
genes <- probeID2nuID(probes, lib.mapping = "lumiMouseIDMapping"[,"Symbol"]
from lumi (I was using lumi for reading/normalizing anyway), but when I started investigating duplicate gene entries and presumably transcript variants, I felt a need to double check the conversion. Does anybody have a suggestion?
By the way, when I try
(380091 being a probe ID for one of genes with name repeated multiple times and with different, according to google, transcript variants) I get
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘columns’ for signature ‘"function"’