How get annotate for Illumina miRNA microarray chips
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3.4 years ago
hejubu • 0

I've been trying to annotate probesets of Illumina Human v2 MicroRNA expression beadchip.Its platforms was said to be GPL8179. But I failed to get the annotation db using the code:

library(annotate)
affydb<-annPkgName(gset@annotation,type="db")
source("https://bioconductor.org/biocLite.R")
biocLite(affydb,character.only=TRUE)

bioconductor failed to return a annotation package named GPL8179.db. I wondere if there really exists a annotation package for this miRNA microarray chip. Or should I build one by myself from the start. I really don't know how to do this. I've been stucked here for a long time and hope some kind suggestions.

My data come from this GEO dataset https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59594

microarray Illumina annotation • 1.1k views
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It looks like you're copying your code from somewhere because you have an object called 'affydb' (Affymetrix), but state that you are using an Illumina microarray.

In which format, currently, are your probe names? - paste an example. Also, you never stated what you want to annotate your data with (MirBase IDs?; micro-RNA target genes?).

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My probes_ID looks like this and I want to convert them into gene symbols or Entrez ID. ILMN_1766650 ILMN_1709593 ILMN_1848383 ILMN_1811387 ILMN_1795342 ILMN_1716400 ILMN_1692938 ILMN_1762883 ILMN_1714741 ILMN_1758816 ILMN_1713892 ILMN_2344971 ILMN_2374425 ILMN_2406656 ILMN_2205050 ILMN_1668108 Thanks for your kind reply.

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