[BioC] quality assessment and preprocessing for tiling array-based CGH data

Leon Yee yee.leon at gmail.com
Wed Oct 22 15:51:24 CEST 2008

Dear all,

     Is there any well-established routine for quality assessment and 
preprocessing of array CGH data, especially tiling array-based CGH data? 
I found most of the quality assessment of array data are about 
expression array, while few are related to array CGH data.
     We are using agilent 244k CGH array of rat, and now we have the 
text files produced by Feature Extraction, don't know whether they are 
of good quality. Could anyone help provide some clues? Thanks in advance!

     After read.maimage(), we got the RGlist object, which contain 
several components including R, G, Rb, Gb, and so on.  The probes are of 
3 types: -1, 1 and 0. 0 means normal probe; -1 mean negative control, i 
guess, and the probe names are like (-)3xSLv1, NC1_00000002, etc[no 
corresponding probe sequence]; 1 means positive control, i guess, and 
the probe names are like DarkCorner, DCP_008001.0, RnCGHBrightCorner, 
SRN_800002, etc[no corresponding probe sequence].  The number of -1 is 
1275, while the number of 1 is 4217, each of which has its R, Rb, G, Gb 
values. Do we need these values for quality assessment and 
normalization? How?
     In addition, in the normal probes, we have 1000 probes repeating 3 
times in the array. How could we use these data for quality assessment 
and normalization?


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