Question: Array CGH quality control
0
gravatar for Noushin N
4.1 years ago by
Noushin N580
Baltimore, MD
Noushin N580 wrote:

Hi everyone,

I am processing a set of array CGH data using fairly standard tools (limma for background correction and normalization, DNAcopy for segmentation).

Some of my samples look quite different in terms of quality by visual inspection. I have included two examples here. I have two questions:

  • Do you know of any tools/ protocols to perform QC on array CGH data?
  • In your experience, can sample DNA quality result in the existing local trends of variation present in sample 1 but not sample 2?

Sample1

Sample2

Thank you!

array-cgh • 1.1k views
ADD COMMENTlink modified 18 months ago by Kevin Blighe56k • written 4.1 years ago by Noushin N580
0
gravatar for Kevin Blighe
18 months ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

Old thread but here comes an answer:

Take a look at arrayQualityMetrics.

Kevin

ADD COMMENTlink written 18 months ago by Kevin Blighe56k
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