I need to do some statistical calculation on CNV data that is publicly available in TCGA website. I am from computer background and no idea about the meaning of these data. I tried searching for the meaning of the files, how they are structured and all but nothing was helpful. It would be nice if someone could give a short overview of the meaning of data in each column. A sample of data present in a CNV file

            Sample	    Chromosome	   Start    	End	    Num_Probes  	  Segment_Mean 
    DEBUT_p_TCGAb45_81_wRedosSNP_N_GenomeWideSNP_6_G03_729530	1	61735	415164	28	-0.0504 
    DEBUT_p_TCGAb45_81_wRedosSNP_N_GenomeWideSNP_6_G03_729530	1	462793	629241	4	1.822 
    DEBUT_p_TCGAb45_81_wRedosSNP_N_GenomeWideSNP_6_G03_729530	1	668210	2138242	350	-0.0311

So I want to know what is the underlying meaning of sample, how they are named. Sample name seems always a big name. Then I understand the columns chromosome, start and end. But I don't understand the meaning of  Num_probes and Segmentation_mean? 

Sample should be the unique sample identifier for this SNP-array experiment, it corresponds to a unique sample run by TCGA and can be a normal or tumor sample. Will map to a unique id like this: https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode

The rows correspond to contiguous chunks along the chromosome with the same DNA copy-number. "Chromosome" is the chromosome, can be 1-22, X or Y (see human genome). Start is the physical start location for the segment along said linear chromosome, end is the end coordinate. Num_probes is the number of SNP-array probes falling within the segment (these were used to call copy numbers). Segment_Mean is the estimated copy number for that particular segment.

So this sample has (log2) copynumber -0.0504 on chromosome 1 from bases 61735 to 417164, at 462793 along the same chromosome the copy number changes to 1.822 (i.e. a genomic gain) and this segment ends at 629241. The next segment for which you have information is 668210 to 2138242 where the copy number has returned to a basically normal level. These segments should keep coming for chr1 until about 255M after which the chr2-segments should start.

The data should basically be log2( intensity of sample / intensity of reference with normal copynumber ), this means that segments with a normal diploid copy number are around log2( 2/2 )=0, single copy losses are at log2(1/2)=-1, homozygous deletions at log2(0/2)=-Inf, correspondingly for gains you go from log2(3/2) and upward with experimental noise leading to deviations from these discrete levels.

For some light reading about the concept of copy-number analysis check out these old papers: https://www.ncbi.nlm.nih.gov/pubmed/16899659 and https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r136 and maybe http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-382




