Entering edit mode
10.4 years ago
mangeles.suarez
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20
Hello,
Does anyone know how to analyze CNVs with the PennCNV package using .CEL files from the Cytoscan HD array? I am in the first step, trying to generate genotyping calls. However, I do not find the way to do it in the APT manual.
Thank you very much.
Are you sure PennCNV is the most appropriate for segmentation of your samples? And what do you need genotype calls for when you want are interested in copy number changes?
I want to compare CNVs with two different softwares and this is one we considered because we started analyzing samples genotyped with the Affymetrix SNP 6.0 array and PennCNV can do it. And the way to do it is following several steps, the first of them, to generate genotyping calls. As these two Affymetrix arrays have output files with the same format, I was looking for a way to analyze CNVs of the Cytoscancan HD samples following the same steps than those used with the SNP6.0 files.
You don't need genotyping calls (AA, AB, BB) to perform copy number analyses, you need the copy number estimates. First step is to normalize the intensities, then to calculate the intensity ratio between your case and your control (e.g. tumor vs blood) and then you segment the log of the calculated intensity ratios. Now what step of the procedure would you like to compare? Normalization, calculating the copy number estimate (which is just a simple division, should be the same with every calculator) or segmentation? What kind of samples do you have? Tumor samples? Then it doesn't make sense to use an HMM segmenter like PennCNV, you are better of with CBS. And why do you want to compare it?
At last, you should have a look into aroma affymetrix. To my knowledge it is the best open source affymetrix copy number analysis package. It can handle many kinds of Affymetrix chips including Cytoscan HD and SNP6.0
I don't have tumor samples. They are from autism patients. I want to compare them with the controls, which were analyzed with GTC + ChAS (Affymetrix softwares) and PennCNV. We used two softwares to know which CNVs are more reliable. So, to compare patients and controls, I would like to analyze patients in the same way I analyzed controls. I understand what you mean when you say i don't need genotypin calls. I mentioned that because is the first step that PennCNV indicates to prepare signal intensity files from Affymetrix CEL files. I don't know another way to prepare the files that PennCNV needs. I'm not familiar with this type of programs. And, I don't find the files specific for the Cytoscan HD array that I need to generate them with the APT. Thank you for your advise about aroma affymetrix. I will take it into consideration.
Did you find a solution? I would like to use PennCNV-affy to extract LRR and BAF values from CytoScanHD .CEL files.
no, not yet. Sorry. If you have any clue, I will apreciated.
Did you manage it to use PennCNV-affy to prepare files for pennCNV from cytoscan hd cel files?
No I didn't, but I found a way to extract LRR and BAF values from CytoScanHD .CEL file using a custom Perl script (see How to read Affymetrix CYCHP File
Hi Mangales, I am also currently working on CytoScan HD array data in my project. Did you find a solution?