How do I get expression levels for transcripts of a gene in Clariom D human Gene chip?

Question

[mailtoshivam13]

Hello Everyone,

I'm analyzing Clariom D human Gene chip assays. During the analysis, I annotated the Expression Data:

transcript.eset.affy <- annotateEset(transcript.eset, pd.clariom.d.human)

I went on with the differential expression analysis using limma and got the differentially expressed transcripts.

However, when I looked at the expression data, different transcripts of any particular genes are always mapped to one probe. For example: TP53 gene has a few RefSeq transcripts, but all of them are mapped to the Probe ID: TC1700009651.hg.1. Looking at the annotated file, the gene TP53 has only one entry which is mapped to the probe ID: TC1700009651.hg.1.

How do I know, for a particular gene, which transcript was differentially expressed between the samples and which one was not?

Any help is highly appreciated.

Thanks a lot!