We used HEEBO microarrays from Stanford Functional Genomics Facility (SFGF) for aCGH. The arrays themselves were designed basically for transcriptome, but we used the arrays to dual up as CGH array, a strategy we used in previous research too.

However, the SFGF has stopped the production and updates of the arrays. The map positions of HEEBO (provided at SFGF site) were of Hg13. Using the probe sequence we assigned the updated map positions to their respective probe IDs. However, for each print batch, the respective postion of the probe IDs differ. To further add to our problem the GAL files of the print batches only provide the Gene names and no probe IDs.

Since we have the exact map location for probe IDs and that most of the genes are replicated (~19000 gene IDs corresponding to 44544 probe IDs), we are not be able to assign the exact map position for the genes provided in GAL file, simply because there will be at least two probe IDs corresponding to single gene.

We solved the problem partly, by searching in submission in GEO database, where we got GAL files of 3 (out of 4 used) print batches, with Gene IDs as well as corresponding probe IDs. We are left with one print batch 'HOAI', for which we are unable to get the GAL file with probe IDs also listed.

If any one has worked with SFGF or HEEBO arrays, I would request their inputs as to where to obtain the GAL files for HOAI print batch which also contains the probe IDs.