Hi everyone,
i am trying to obtain the gene symbol from Affymetrix probe "hgu133ahsentrezgcdf". I have tried several strategies but with no luck. i have obtained the expression profile from the GSE45642 but now i can´t identify the gene symbol of probe IDs.
Thanks
Dear Filipe Ricardo Pires Carvalho
It seems that there is no annotation library for "hgu133ahsentrezg" in bioconductor (like hgu133a2.db). But I hope that the below link may help you where they have used a custom library for hgu133ahsentrezg.
https://www.biostars.org/p/61987/
If nothing works out,... you can use DAVID to convert Affymetrix probe ID to Gene Symbol. Step 1: Paste the Affy Probe ID in the "enter gene list" box. Step : Select Official gene symbol as identifier and Submit.
DAVID will automatically recognize the probes and helps in converting them to Gene Symbol.
Dear Filipe Ricardo Pires Carvalho ,
If your query is limited to convert Affymetrix probe id into gene symbol use the tool GEO2R.
Secondly, the best option is to use DAVID (https://david.ncifcrf.gov/conversion.jsp ) or Biomart (https://www.ensembl.org/biomart) to convert the Affymetrix probe ID into gene symbol.
You can use the GPL file that's included along with the GEO record:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL17027
The SPOT_IDs are Entrez IDs. Using them you can easily get the gene symbols. You can use the gene_info file to get gene symbols for Entrez IDs: ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
Alternately, you can also try using DAVID's gene ID conversion tool, as others suggested, to get gene symbols from affy IDs:
https://david.ncifcrf.gov/conversion.jsp
Dear Premanand A. , Fareha Masood and Anil Jegga thanks you all for the great help.
I have tried every solutions to find the gene symbol of my list (biomart, DAVID, GEO) but all of them add few probe id for "hgu133ahsentrezg". The solution was as you said Anil Jegga , i used the GPL file and than found affymetrix_IDs and the Entrez IDs.
Thanks you all.
1. Make sure which platform the authors used by looking at using GEO accession number: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE755
2. Download related libarary from http://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData
3.Run the following R code
library(Biobase)
library(GEOquery)
library(annotate)
library(hgu95av2.db)
select(hgu95av2.db, c("1007_s_at","1053_at"), c("SYMBOL","ENTREZID", "GENENAME"))
Thanks Hong, its always good to now.
Very well explained.
Cheers
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