Hi Nikhil, Your observations are consistent with what I have seen before with Illumina data. They have more probes on the array (and in the bead-level data) than are reported in BeadStudio or in the annotation files. There could be a few hundred of these. I understand them to be internal controls of some kind and probably not informative for your analysis. In answer to your other question; the ProbeID column does indeed correspond to the Array_Address_Id column in the annotation and you are looking at it the right way. It's unfortunate but probably a symptom of the way they keep changing the format of their files. In addition to Marc's response, you could also consider using the following annotation packages which has these ProbeIDs/Array_Address_Ids as a key. http://www.bioconductor.org/packages/release/data/annotation/html/illu minaHumanv3BeadID.db.html Hope this helps. Regards, Mark On Wed, Apr 29, 2009 at 7:07 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Nikhil, > > What do you have installed? ?Can you give us the output of sessionInfo()? > > > Since you are using bioconductor, you might want to have a look at the > annotation package that is maintained for this platform: > > http://www.bioconductor.org/packages/devel/data/annotation/html/illu minaHumanv3.db.html > > > > If you want some help in how to use that package, you might also look at > the AnnotationDbi package: > > http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.h tml > > > And finally, if you should discover that your HT platform is > significantly different from what has been offered by illumina before, > you could even build a custom annotation package by following the > instructions in the SQLForge vignette (which you will also find along > with AnnotationDbi). > > > > ?Marc > > > > > > Nikhil Joshi wrote: >> Hi all, >> >> This is my first post, so please bear with me. ?I was not able to find >> any information regarding this in the archives, so I am posting here. >> I am doing a differential expression analysis using three Human >> Sentrix chips in R, utilizing the beadarray package. ?I am then using >> the Human annotation file from Illumina (i.e. >> HumanHT-12_V3_0_R2_11283641_A.txt) to match Probe >> IDs/Array_address_IDs to GI numbers. ?So here are my questions: >> >> 1. In R, when I load my data using readIllumina >> (backgroundMethod="rma", normalizeMethod="quantile", >> annoPkg="Humanv3"), the data that I get has data for each of the >> arrays, and within an array there is a column called "ProbeID". >> However, this ProbeID seems to correspond to the Array_address_ID >> field in the annotation file, even though there is a field in the >> annotation file called Probe_Id! ?Can anyone explain why the ProbeID >> in R does NOT correspond to the Probe_Id field in the annotation file, >> but instead corresponds to the Array_address_Id field? ?Am I looking >> at this incorrectly? >> >> 2. After I do my differential expression analysis, I get data for my >> top results. ?These results include a ProbeID field. ?Most of these >> ProbeIDs have entries in the annotation file, however, about 300 do >> not. ?I looked for the probes in the R data, and I found that they did >> exist and the replication was just as much as all of the other >> probes. ?Which leads me to believe that they are actual probes, and >> not some error of some kind. ?So my question is, why don't these >> probes have annotation information associated with them in the >> annotation file? >> >> Any help is highly appreciated. ?Thank you! >> >> - Nik. >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >