Processing With Snp6 Cel Files Into Cn Segmentations

Question

[J.F.Jiang]

Hi all,

I am facing a problem to obtain the segmentation files for probes in SNP 6.0 files, I mean to obtain the log2ratio for the probes.

As far as I know, I can use GTC or dChip to obtain the segmentation values, however, I still do not know how to run dChip though they offered a tutorial for SNP arrays.

My question is that is there any other tools that can process the raw CEL files, e.g., R packages or tools in linux?

Thanks,

Answer 1

[Charles Warden]

DNAcopy is a popular tool for making copy number calls:

http://www.bioconductor.org/packages/2.13/bioc/html/DNAcopy.html

I personally haven't worked with raw SNP 6.0 array data, but it looks like this package might be able to help you extract the data so that you can analyze it with something like DNAcopy:

http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html

There is also this related post:

How to use affy SNP6.0 data with BRB-ArrayTools or CGHTools?

[J.F.Jiang]

Thanks, DNAcopy is a commonly accept CBS tool, while it requires a signal intensity (log2ratio) for each probe as the input. It seems that the tools you mentioned did not take the reference CN into consideration.

Just like GTC, RAE or GISTIC, they will take the tumor-over-normal log2 intensities by substracting the tumor value by the normal ones, e.g., the HapMap samples under the same platform.