How can I transform CNV output data of Agilent 244K to TCGA/GDC data?

Question

[titiro89]

Hi everyone, I am trying to work with Copy Number Variations (CNV).

I have samples for aCGH analysis using the Agilent 244K Chip by Myriad Genetics. Every sample is structured in this way:

1  -0.055518725
2   0.085221382
3  -0.650189314
4   0.085176382 
5   0.007979838
6   0.089254443
7   0.078943541
8   0.02681327 
9   0.200645608
10 -0.306892726
................
................
243499  -0.034404618
243500  -0.052923749
243501   0
243502   0
243503  -0.014568005
243504  -0.040646156

I don't know how to work with these data, because I didn't find any documentation, I don't know the meaning of the columns. So:

1) Can anyone give me a help, maybe telling me where I can find a good documentation for the output of Agilent 244K?

I have always worked with data stored in this way (this is an example of TCGA/GDC data of CNV, obtained as an output of Affymetrix Genome-Wide Human SNP Array 6.0):

Sample  Chromosome  Start   End Num_Probes  Segment_Mean
EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6  1   61735   17112177    8814    -0.0283
EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6  1   17114427    17262247    69  0.3902

My goal is to transform the data obtained from Agilent 244K (like the example above at the first point) into a more "friendly" structure as the data that can be downloaded from TCGA/GDC .

2) Where can I find a tool/script/algorithm that can transform the data as I want?

Thanks in advance.

Answer 1

[Titus]

Hi,

May be the first columns is the reference of the probe , and the second the log ratio of the signal ?

Best

[titiro89]

Hi, but how can I relate these probes to coordinates such as "Chromosome", "Start" and "End"?

[Titus]

Don't you have the "map" of the Chip and the corresponding coordinates ? In our case my colleagues use a software named CytoGenomic they give it a sort of bed but the probe names are not a single number. Maybe try to ask Myriad Genetics , i could be by anything without columns names :(

I tried to find information about CGH-array Agilent but like you i wasted my time ...