Hello,
I am new to R and new to Bioconductor. I have a list of GEO samples (GSMs) that I would like to process and combine using Barcode in R (http://barcode.luhs.org/index.php?page=search) to identify which genes are expressed or not in my tissue of interest (i.e. binary).
I installed all the required packages and I used the test data as follows:
data(AffyBatchExample)
object <- frma(AffyBatchExample)
bc <- barcode(object)
However, I am not sure how to input my list of GSMs to obtain a single combined list of unique expressed vs not expressed genes. Ideally, if possible, using Entrez Gene IDs. I would really appreciate it if anyone would be able to help me please.
This is my list of samples:
GSE8397 (GSM208648, GSM208650, GSM208635, GSM208649, GSM208630, GSM208651, GSM208647, GSM208632, GSM208633, GSM208631, GSM208652, GSM208646, GSM208645, GSM208634); GSE7621 (GSM184359, GSM184361, GSM184357, GSM184362, GSM184354, GSM184355, GSM184360); GSE20292 (GSM508721, GSM508708); GSE20291(GSM508688); GSE20164 (GSM506014, GSM506020, GSM506019, GSM506023); GSE20163 (GSM506008, GSM506007, GSM506003, GSM505999, GSM505998, GSM505997, GSM506001);
Thank you already so much for any help provided.
Best wishes,
Diana