Hello everyone,

I know that affymetrix probeset ids are portable across platforms: the same probeset id `1090_f_at` always refers the same gene (probe set). Is it the same for probe ids?

Executing, as discussed in the "affy" package vignette, the code:

    > pm(Dilution, "1090_f_at")

on the chip HG_U95Av2, for the probeset 1090_f_at are returned its pm probes 1, 2, .. 16

```
                            20A 20B 10A 10B
1090_f_at1          115.0 74.0 94.0 61.0
1090_f_at2          129.3 80.3 108.0 70.3
..
1090_f_at16         262.0 157.0 194.8 131.5
```

Executing the same code on a different chip containing, of course, the same probeset `1090_f_at`, are its pm probes returned in the same order, so that their ids

```
1090_f_at1,
1090_f_at2,
..
1090_f_at16
```

are consistent across chips? 

I suppose so. Could anyone confirm it? How could I check it?

Thank you
It may depend on the source of the file you are using to obtain probe ids. Probe IDs in files from Affymetrix are integers and are associated with a specific feature (x, y position) on the microarray. For clarity this is different than a probeset id. A probeset id refers to a collection of probes (you seem to know this difference but I see people use the terms probe and probeset interchangeably in casual conversation which leads to confusion...)

Probe IDs for Affymetrix arrays (in files released from Affymetrix, this may differ depending on the creator of your analysis package) are often calculated based on a formula and convertible from the probe id to an x y coordinate on the microarray.

Therefore the only reason a probe_id should be the same between two different arrays is if the probe is the same height and width, and the probe is at the same x, y coordinate on the microarray. (This is rare).

You can download lots of information from the Affymetrix website. If you have any further questions just ask. I'm pretty familiar with it.