How To Regenerate Cel Filed From Dat Files (Affymetrix Microrrays)

Question

[Maria K]

I scanned Affymetrix Mouse Gene 1.0 ST microarray and chose the option "Human Gene 1.0 ST" by mistake. Now all the CEL files generated after scanning by AGCC are meant to be human CEL files, but they are mouse files. I tried to change the probe array type in AGCC (there is a standart function), something happened, but the CEL files remained the same and are read as Human CEL files by genotyping console.

I thought it might be possible to regenerate CEL files from the DAT files (as they are raw images they should be correct anyway) but I couldn't find how to do it via AGCC or any other software. I would greatly appreciate if anyone could help me to solve this problem.

[Michael]

It might be possible somehow, but you are likely to create a mess on the way (maybe even unnoticed). Especially since it is in a binary format. E.g. what if the scanned arrays have different number of rows,cols and different calibration positions for example? Anyway, if it helps: http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html

[Maria K]

Thank you, Michael! I understand that it could be difficult and likely to cause additional errors and mess, but I still hope there is a way to cope with the problem, at least somehow. Actually Affymetrix provides a single file describing all Gene 1.0 ST arrays design (human, mouse and rat), what makes me hope that technically they are the same (I mean calibration positions etc.). I couldn't find any further information about the differencies between human and mouse arrays. Addresed this question to Affymetrix, waiting for an answer from them. Anyway, thank you for your attention and help.

Answer 1

[Maria K]

According to oficial information from Affymetrix, it is possible to re-generated the CEL file with the correct library files (assuming that the microarray type is the same, as in this case - Gene 1.0 ST for example). This is possible as the arrays in question have the same feature size.

You first need to open the AGCC portal.On the DATA menu choose folder view. Select the array in question by ticking it and choose 'change probe array type' on the 'command to run' menu.

It is required to have the latest version of AGCC software and the proper library files for Mouse Gene 1.0 ST.