I am trying to code my own routine to extract probe set information from the CDF for the Human Gene 1.0 ST Array http://www.affymetrix.com/estore/esearch/search.jsp?Ntt=cdf&basic=1
I do not understand how the CDF file relates to my CEL files. http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html
I can see that within each block there are indices which presumably correspond to the indices of the probes in the CEL file. But I do not understand how the terms "block", "atom" and "cell" relate to the probes on the microarray.
I also do not understand the layout of probes on the microarray. Are perfect match and mismatch probes spatially related? (i.e. perfect match is always above mismatch) Are probesets in the same spatial area? (I would guess not for randomisation.)
Thanks, Stephanie
Example Block Below:
[Unit7892501] Name=NONE Direction=1 NumAtoms=4 NumCells=4 UnitNumber=7892501 UnitType=3 NumberBlocks=1
[Unit7892501_Block1]
Name=7892501
BlockNumber=1
NumAtoms=4
NumCells=4
StartPosition=1
StopPosition=5
CellHeader=X Y PROBE FEAT QUAL EXPOS POS CBASE PBASE TBASE ATOM INDEX CODONIND CODON REGIONTYPE REGION
Cell1=870 110 N control 7892501 0 13 G C G 0 116370 -1 -1 99
Cell2=28 899 N control 7892501 1 13 T A T 1 943978 -1 -1 99
Cell3=638 469 N control 7892501 2 13 A T A 2 493088 -1 -1 99
Cell4=888 863 N control 7892501 3 13 T A T 3 907038 -1 -1 99
