Hi everyone, I have a transcription dateset in the format HG-U133_Plus_2 affymatrix and I want to convert it into official gene symbols. I have tried bioconductor "hgu133a.db" library but it doesn't work. Can somebody help me out understanding how to do it? I put here some of the probes I'm unable to convert. Thanks in advance!
1552256_a_at 1552257_a_at 1552258_at 1552261_at 1552263_at 1552264_a_at 1552266_at 21552269_at 1552271_at 1552272_a_at 1552274_at 1552275_s_at 1552276_a_at 1552277_a_at 1552278_a_at 1552279_a_at 1552280_at 1552281_at 1552283_s_at 1552286_at 1552287_s_at 1552288_at
1. using notepad replace the at with space
2. copy the whole file to any biosoftware, which will omit the number and _, then you got the gene file.
Go to NCBI Gene Expression Omnibus portal of HG-U133_Plus_2 at:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570
Scroll down to bottom of the page, there you will a link 'Download full table'. Download the table which is about 76MB. Open the file in excel, and filter/find your Affimatrix IDs with HUGO gene symbols in the table.
Cheers
Dear Riccardo;
A) the database of DAVID can convert the affy IDs.
B) If you are not skilled in programming:
1) download the latest annotation file for HG-U133_Plus_2 from the company website:
currently at: http://www.affymetrix.com/support/technical/byproduct.affx?product=hg-u133-plus)
find the file named
HG-U133_Plus_2 Annotations, CSV format, Release 36 (36 MB, 7/12/16)
2) unzip the file
3) open the file in MS excel
4) use "vlookup" function of excel to find the symbols. If you have a handful IDs you may search within the file.
If familiar with coding in R, then use annotationDbi (Bioconductor package)
Best
You can also achieve this conversion using the Batch Query tool in Affymetrix's NetAffx Analysis Center. No special informatics skills are needed.
https://www.affymetrix.com/analysis/index.affx
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