I am working with some gene expression data that was collected using Gene Chip Human Gene 1.0 ST Arrays according to Affymetrix standard protocols. Paper was published in 2013. There is an old annotation file that contains probe ids mapped to gene names. However a newer annotation shows differences in the probe data. Meaning some of the probes map to different genes.
As an example, in the old data, probes that don't map to anything now are annotated to certain genes. Some of these are shown below:
id gene.name.orig gene.name.new 1 7892501 SNORD58B 2 7892501 RPL17 3 7892506 TARDBP 4 7892508 RNPS1 5 7892509 HSP90AB1 6 7892512 JTB
Should we use the more recent mappings or use older mappings?