Extracting Data With Biomart / Problems

Question

[pcmubs]

I try to use biomart http://www.ensembl.org/biomart/martview/ to translate a list of Affy HuGene 10 st v1 probeset IDs to something I can work with (like EnsemblGeneID). When I upload a list of 324 probeset IDs to "Filters" > "Gene" > "ID list limit" and click on the buttion "Count" the website shows that the dataset is only 175 genes long. When I export unique Attributes like "EnsemblGene_ID" i get 175 unique results. Where are the missing 167 genes / positions? Im quite sure that all of the probeset IDs are correct. Thank you!

[Irsan]

When you click results and at the attributes tab you say you want to get probe id and gene name/id back you will get a list of all the probes mapped to the genes. When you sort that on probes you will see that multiple probes map to the same gene. Addtionally you could use sort | uniq -d on the gene column to get the genes with multiple probes

Answer 1

[Istvan Albert]

Multiple probes may map to the same gene. That probably explains what you see.