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Leon Yee
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110
@leon-yee-3088
Last seen 10.2 years ago
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?
Regards,
Leon