I need to get the gene library for R bioconductor. Is there a way to get the library name (like HsAgilentDesign026652) from the probe name (like A_33P3388745). My code uses both R and python so a way in either language could help.
Thank you.
If you want to obtain the total probeset for the array that probe came from your best option is to obtain the annotation files from Agilents eArray utlity. I'm not sure that you can automate retrieval from this website but it is the most up to date annotation available.
If you are just interested in the transcripts these probes target, use Ensembl's microarray probeset mapping service (http://useast.ensembl.org/info/genome/microarray_probe_set_mapping.html). You can automate obtaining data from here with Python if you are familiar enough with MySQL, or using Biomart with R. The advantage here is that you will get all of the transcripts the probe targets, not just a single gene. This will provide more detailed coverage of the items targeted by that probe than gene annotations alone.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
You should go to their website and look for annotation for that specific platform.
I am having no trouble getting anotations in R using bioconductor, but I need the library bimap name first. I am currently using google and some detective work to find the libray name (not very automatable).