[BioC] quality assessment and preprocessing for tiling array-based CGH data
yee.leon at gmail.com
Wed Oct 22 15:51:24 CEST 2008
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
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
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