Hi Denise, This question was raised by other people before. Here, I just CC this email to Bioc mailing list, so other people can also know the reason. First, I need to clarify how the annotation packages were created. Here is the building process of Bioconductor annotation packages: Probe Id --> refSeq Id / Unigene Id --> Entrez Gene Id -- > annotation At each step, the mapping could be missing. For example, for the whole-genome chips, about half of probe Id to refseq mappings are missing because lot of probes were not designed based on refseq database. or updating of refseq database The lumi ID mapping packages provide mapping information of probe Ids to refSeq Ids. Lots of probe ids have no refseq id mapping available due to the reason I just mentioned. When mapping refseq Id to Entrez Id, still there are some mapping missing (might be due to the obsolete ids or update of Entrez database). I think this can explain the problem you found. Pan On 11/5/08 7:35 PM, "Denise Mauldin" <dmauldin@systemsbiology.org> wrote: > > Hello, > > I loaded the information from the lumiHumanAll, lumiMouseAll, and lumiRatAll R > packages and the HumanIDMapping and MouseIDMapping packages into a database. > When I'm doing a comparison between the tables, I find that there are 22,468 > nu IDs that are in the lumiXXAll packages and not in the IDMapping packages, > which is likely due to the fact that there is no RatIDMapping package. > However, when I look for nu IDs that are in the IDMapping packages and not in > the lumiXXXAll packages, I get 268,761 IDs. > > For example, nu ID 'uMDxBs4BOkJwTJzwQo' is present in MouseWG6_V1, > MouseWG6_V1_1_R2_11234304_A, MouseWG6_V1_B, and MouseWG6_V2_0_R0_11278593_A, > however it doesn't have an entry in the lumiMouseAll package. This means that > I don't have an entrez gene ID for that nu ID. Are these errors because there > is no information for 268,761 of these IDs? > > I've attached a list of these IDs in case I'm doing something incorrectly. > > Thanks, > Denise > [[alternative HTML version deleted]]