Affy 6.0 - Number of Probes per Chromosome

Question

[gaiusjaugustus]

I am doing an analysis of TCGA's CNV data. I'd like more information about the probe density on each chromosome of the Affy 6.0 array used by TCGA; I'll be comparing that to my data, which was done on a different Affy platform.

Does anyone know where I can find out how many probes there are per chromosome on the Affy 6.0 chip?

Answer 1

[AndreiR]

If you look for affymetrix documentation: http://www.affymetrix.com/Auth/analysis/downloads/na35/genotyping/GenomeWideSNP_6.na35.annot.csv.zip I think you should find something like that:

73403  1
49592  10
45933  11
43797  12
35143  13
28939  14
26865  15
28622  16
21300  17
27213  18
12419  19
75842  2
23486  20
12910  21
11951  22
62277  3
57556  4
57945  5
57818  6
48283  7
49992  8
42663  9
411    MT
37902  X
860    Y