Hello Group, I am new to Microarray data analysis and statistics. In microarray group circles people are talking about raw data, un-annotated raw data and annotated raw data. Could any one please help me in explaining what exactly means annotated raw data. Is this some thing to say that a particular spot gene name is "xxx" and it has some intensity levels xxx(ch1) xxxx (ch2) etc. If this is what is annotation component then the microarray raw data (cDNA) already has intensity levels linked to a gene and not some arbitarary code number. Could any one please post their understanding about annotated data. thank you. Ranga --------------------------------- [[alternative HTML version deleted]]

Ranga, I think you already have the idea. However, I have no idea why someone made a big deal of the distinction to you. Clearly, the only reason that microarrays are useful is that they link expression levels of (somewhat) known quantities to biological knowledge bases. Usually, as you point out, one knows the "identities" of the spots on a microarray (cDNA, oligo, BAC, whatever) BEFORE one does the hybridization, so I can't think of a situation where one has only raw data with NO annotation. Even in the case of a truly unknown EST, one still presumably has a sequence (or a way to retrieve it) so that tools like BLAST, HMMER, etc. are available. Therefore, I think that the distinction here may be the way that the annotation is handled in processing the raw data into useful biological information. Sometimes, that is quite straightforward, and sometimes it requires a devoted bioinformatics team. This is to be distinguished from retrieving the annotation and using it for analysis. Clearly, this is often another major bioinformatics feat (one might argue that this is THE largest challenge in using microarray technology right now) which BioConductor attempts to answer with the various annotation packages. Sean On 6/29/04 9:10 PM, "Ranga Chari" <ranga_bioc@yahoo.com> wrote: > Hello Group, > I am new to Microarray data analysis and statistics. In microarray group > circles people are talking about raw data, un-annotated raw data and annotated > raw data. > Could any one please help me in explaining what exactly means annotated raw > data. > Is this some thing to say that a particular spot gene name is "xxx" and it has > some intensity levels xxx(ch1) xxxx (ch2) etc. > If this is what is annotation component then the microarray raw data (cDNA) > already has intensity levels linked to a gene and not some arbitarary code > number. > > Could any one please post their understanding about annotated data. > > thank you. > Ranga > > > --------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Hello, I would like to normalize data from fifty chips with the RMA method. The problem is that I have both U95A and U95AV2 chips which seem to differ from around only fifteen probesets. Has anyone already encountered this problem? Should I have to remove the probesets (on the CEL files) which are not the same in the chips, and normalize only the others? Thanks a lot for your help, Regards, Willy