containing the mapping database are missing some 9300 accessions (ILMN_) identifiers for the chip I used for microarray.
I have loaded the bridge files from 2007 till 2016 and still some genes are unrecognized.
This is why I am asking if there is a way to translate/convert all of the ILMN_ identifiers into another platform like Agilent/Affymetrix/RefSeq which I could use when uploading my expression data in PathVisio.
Is there any R package and script that might help me in this respect. I am not IT and have minimum experience with R so your help would be very much appreciated.
There are certainly ways of doing this from R using bioconductor packages. If you start by importing your data into R you can then use the annotation package "illuminaHumanv4.db" to convert illumina probe names to other identifiers.
# install the package
# load library
# your_probe_ids <- import(expressiondata)
# The below function call will return a datafram with probe_id, gene symbol
# and ŕefgene_id for your data
keys = your_probe_ids,
Note that there are probes on the array that can not be converted
to gene ids, there is for example many control probes on the
This is more or less directly from the vignette "1. Introduction
To Bioconductor Annotation Packages" that is part of the AnnotationDbi package