From TCGA microarray CNV data, which is level_3 data with segment means, if I use the CNV package, how to analyze and out put the results? For example I just compare the tumor sample and the normal one in Chromosome 11, or the whole genome, how to compare ? Many thanks.
You have many ways to do it, one of which is CNVkit.
Get all chromosome positions from the Level_3 file scu as cut -f 2,3,4 input_Level_3_File | grep -v Chromosome > location.txt
cnvkit.py target --annotate refFlat.txt -o annotated_location.txt location.txt ( The refFlat.txt can be downloaded based on the reference in CNVkit documentation.)
Do you mean the CNVkit software package, or some other specific software?
The TCGA level 3 copy number data are in SEG format. With CNVkit you can import these segments to CNVkit's segment format using "cnvkit.py import-seg". From there what you do depends on your research goals.
Many thanks, Etal. in fact I just need to make a matrix of gene information of CNV according to Level_3 data from comparing Normal sample (10 A ) segment mean and Tumor sample (01A) segment mean, for example, the threshold is -0.2 and 0.2. How to download the reference file correlated to Level_3 file which can provide gene symbols? What tools can be used? Many thanks.