Hi Kathleen, One of our engineers had these comments: "If these probes don't map to any human genes, and have identifiers that follow a distinct naming convention, they're probably something like bacterial control probes. Part of the assay involves spiking in some bacterial material, not found in the human genome. The intensity measured at these control probes gives one a way to verify that the chip was more or less hybridized correctly, and can help with normalization. Since the GNF Atlas was a custom Affy chip, Affy wouldn't maintain information on these probesets. But someone would have information on the probesets (GNF?), for verifying that these are in fact controls."
Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 7/11/11 10:24 AM, kathleen askland wrote: > Hello, > I've corresponded a few times with the mailing list regarding my attempts to > may the 44,775 probes in gnfHumanAtlas2All dataset to genes and appreciate > all of the helpful responses. > I have a follow-up question that I was hoping someone may be able to answer > for me: > Most of the probe IDs in the dataset have a format that begins with a > number, followed by '_at' or '_x_at'. Through a series of merges, I have > been able to map the vast majority of these probes to one (or more) genes. > However, there are over 13,000 probes whose probe ID begins with 'gnf1h', > followed by a number and '_at' or '_x_at' (e.g., gnf1h22472_at, > gnf1h22473_x_at). I have been unsuccessful at mapping these 13,000+ probes > because the IDs do not appear in any mapping set I have found. Can I assume > that the characters following the 'gnf1h' correspond to the actual (more > standard) probe ID and use that for mapping to genes? > Thank you, > Kathleen > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
