Question: How can I transform CNV output data of Agilent 244K to TCGA/GDC data?
gravatar for titiro89
3.1 years ago by
titiro890 wrote:

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.

affymetrix cnv tcga snp agilent • 987 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 3.1 years ago by titiro890
gravatar for Titus
3.1 years ago by
Titus910 wrote:


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


ADD COMMENTlink written 3.1 years ago by Titus910

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

ADD REPLYlink written 3.1 years ago by titiro890

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 ...

ADD REPLYlink written 3.1 years ago by Titus910
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