How Many Probe Set In Each Chip?

Question

[Fahmida Yeasmin]

How many probe set in a single Chip?Or a chip is itself a probe set? I am confused...

Answer 1

[Chris Evelo]

While Ketil's and Pasta's answers are formally correct, a probeset is in principle any set of probes, the word probeset is usually used in relation to Affymetrix microarrays. For Affymetrix a probeset is a set of probes that target a single gene. Affymetrix used short (25mer) oligo probes as reporters on their microarrays that are synthesized on the arrays using photo lithographic procedures. Because the probes are short you need more than one to get a clear signal for an individual gene or gene transcript. Older (type 1 and type) Affymetrix arrays were designed to use 11 probes per probeset, they also used one so called mismatch probe for every real probe. They sometimes had more than one probeset targeting a single gene. This and the fact that some probes were found to not or not uniquely hit the target sequence (or not in the right direction) let to annotation updates in the form of so called custom .cdf's where both the total number of probesets (typically one per gene) and the selection of the probes used in a specific probeset can be different from the original design. Custom .cdf's have been discussed in a number of other BioStar questions.

The newer Affymetrix WT arrays can contain probesets that are targeted to single exons (the so called exon arrays) or that cover all exons of single gene (the so called ST gene arrays).

You might want to check out the presentations about Affymetrix technology that I used recently during our course in Sao Paolo. They consist of a [?]general introduction[?] and a [?]set of slides about the newer arrays[?] and the differences compared to the older ones. These slides I received directly from Affymetrix after [?]another question here on Biostar[?]. This last presentation also contains the literal answer to your question how many probsets there were (designed to be) on the different types of Affymetrix arrays. There were 54,000 on the Human U133 type 2 arrays (which you find a lot in e.g. GEO) and a whole 1.4 million on the new WT exon arrays. The other presentations we used during the Sao Paolo course are also [?]available on our wiki[?].

Answer 2

[Ketil]

Normally a probe set (for a microarray) is just that, a set of probes. So you could include several probe sets on a chip, as long as there's space for it.

Answer 3

[Pasta]

Well, it all depends what kind of array you are talking about. A probe set is a group of probes, obviously. Let's say that you work with the Agilent technology and that you have 22.000 probes. This is your probe set which makes 1 array (or chip). Now this probe set can be repeated 4 times, for ex., on the SAME glass slide. So 1 glass slides can have several probe sets.

Answer 4

[Fahmida]

many many thanks Pasta,Ketil and Chris Evelo...Now I understand the problem. I may ask you more question later and hope that you will answer them...hope to see you there, take care.