Hi,

I am working with HT_HG-U133_PLUS_PM Chip Definition File. I found hthgu133pluspmcdf and hthgu133pluspmprobe. But I could not find hthgu133pluspm.db. I have done a literature search and looks like we can build the package. I am not sure how to do the annotation database. I have looked at the vignettes of AnnotationForge but I could not do it. 

Could somebody help me in getting the annotations of this chip.

Thanks,

Prat

There are two ways to approach this problem. First, you can go the easy way, which is to note that the probeset IDs on the HT_HG-U133_PLUS_PM arrays are identical to those on the conventional U133_Plus2 array, except for the addition of an extra _PM in the probeset name. Because obviously Affy would want to do something like that. There are some small differences in that there are fewer  probes for some probesets (and obviously no MM probes), but altogether, other than 40 extra QC probes, the arrays are very similar. And are intended to measure the same thing.

So you could just process the data as normal, then remove all the '_PM's from the probeset IDs and use the hgu133plus2.db package to annotate. That's probably what I would do.

An alternative would be to get the annotation csv file and then build your own annotation package. We can certainly help you with that task, but would need more information than 'I could not do it', which could mean any number of things.

In other words, this is an old array that you can't really get any more, so it's not in anybody's interest to make the annotation package, especially since you could make do with an existing one. So you will have to do the legwork to make it. If you show what code you used to try to make the package on your own, then we can give pointers as to where you went wrong. But like I said, it's way easier to just use the existing annotation package.

When I tried to process the CEL files of this chip, I tried using "gcrma" normalization method, it is throwing me the following error 

Error in matrix(NA, nrow = max(cbind(pmIndex, mmIndex)), ncol = 1) : 
  invalid 'nrow' value (too large or NA)

But if I use "rma", I am able to successfully normalize the data. And I am successfully able to change the featureNames and could map all the annotations. 

Thanks,

Prat