What is probe number and segmentation mean in copy number variation(CNV) data

Question

[akij]

In TCGA Copy number variation(CNV) data there is a column with title Num_Probes. What is the meaning of probe number with respect to the sample data below?

Chromosome  Start   End Num_Probes  Segment_Mean
1   61735   62152   4   1.1973
1   62920   12777697    6514    2.2882

According to wikipedia, probes are usually 100-1000 bases long. Then does it mean in the first row above that, it took 4 probes to identify the region(61735 - 62152). In that case what would be the meaning of Segment_Mean?

Answer 1

[Eric T.]

The TCGA data is usually from array CGH, which is a microarray assay. Each probe registers an intensity, which relative to a baseline implies the copy ratio estimate for that probe -- usually represented in log2 scale, so 0.0 indicates neutral or normal copy number. Segmentation groups together adjacent probes likely to have the same copy number in the sample's genome. In this output format (see SEG), Num_Probes is the number of probes assigned to a segment, and Segment_Mean is the arithmetic mean of those probes' log2 copy ratio values.

[sbt_gvs]

@Eric T How do we use the above data and then create cnv plots ? is there a package or blog post that talk in detail how to analyse and plot ?