In a probe cell ,the probe IDs are all the same?

Question

[Joe_daisy]

I want to know ,in a probe cell ,the probe IDs are all the same? usually ,how many probe IDs are in a probe cell? thx~

Answer 1

[Chris Evelo]

I think your questions is about probe sets on Affymetrix microarrays, right? And the question is whether all probes in a probeset are the same? No they are not. The trick is that every probe targets a different part of the RNA and has different specific binding properties (and sometimes different sequence specificity). On exon arrays that can even be used to target the individual exons. By design the number of probes in a probe set is the same for a whole array but can differ between array types. You can read about Affymetrix probeset design on their website, starting here. Note that people often use custom probe set annotations, as was discussed in several other posts. In that case the number of probes per probe sets can vary because of removal of bad or a-specific probes or because probe sets are merged.