Hello everybody,
There are a couple of posts that talk about tackling the problem of mulit-probes targeting a single transcript/gene, and as I found, taking the medium or mean of the expression values would be a good solution. So that's OK, but my problem is that I have some probes that target several transcripts, so that I cannot figure out how to select a transcript to be representative of that probe.
To be more specific, I am working on a microarray probeset with Agilent platform, which is designed to target some human coding and non-coding RNAs. I used BLAST against a local non-coding RNA database, and found that some probes target more than one transcripts (though they are from one single gene)
I should add that my choice to work on "transcripts" level rather than "genes", was due to the fact that there may be a differential expression in one transcript from a gene, but not for other transcripts for the same gene, and so any method to integrate expression values for these transcriptions, may undervalue the importance of that gene.
Thank you for your response. Actually, I finally decided to consider the whole gene, because of the limitation that you mentioned. But my next problem was how to select among or combine those probes that target a gene, which in my case, my solution was to select the probe with most variant expression values in its cases. Others may prefer to combine probes by getting an average/medium among their expressions.
You may want to be careful with how you decide which probe changes the most. Keep in mind that you can get very large fold change values from probesets with very low signal. You probably need to set a minimum threshold for expression before using fold change to base your selections on.