Question: How Can I Use Penncnv With Samples Genotyped With Cytoscan Hd?
2
gravatar for mangeles.suarez
5.4 years ago by
mangeles.suarez20 wrote:

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.

• 3.2k views
ADD COMMENTlink modified 4.2 years ago by sam0 • written 5.4 years ago by mangeles.suarez20

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?

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Irsan6.8k

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.

ADD REPLYlink written 5.4 years ago by mangeles.suarez20

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

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Irsan6.8k

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.

ADD REPLYlink written 5.4 years ago by mangeles.suarez20

Did you find a solution? I would like to use PennCNV-affy to extract LRR and BAF values from CytoScanHD .CEL files.

ADD REPLYlink written 5.2 years ago by Christian2.8k

no, not yet. Sorry. If you have any clue, I will apreciated.

ADD REPLYlink written 5.1 years ago by mangeles.suarez20

Did you manage it to use PennCNV-affy to prepare files for pennCNV from cytoscan hd cel files?

ADD REPLYlink written 4.9 years ago by hongen.hugo.xu0

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

ADD REPLYlink written 4.9 years ago by Christian2.8k
2
gravatar for Matt Shirley
5.0 years ago by
Matt Shirley8.9k
Cambridge, MA
Matt Shirley8.9k wrote:

Take a look at this project that Carles Hernandez has on Bitbucket: https://bitbucket.org/carleshf/affy2sv/wiki/CytoScan. It's an R package that allows you to process the Cytoscan CEL files and produce input tab-delimited files for PennCNV, MAD, and PLINK.

ADD COMMENTlink written 5.0 years ago by Matt Shirley8.9k
1
gravatar for kuragari.ch
5.0 years ago by
kuragari.ch20
Spain
kuragari.ch20 wrote:

Hi!

I don't know if it could help you, but there is an R package (that warps APT... ) to create files for PennCNV and for MAD. May be it can help you.

 

ADD COMMENTlink modified 4.8 years ago • written 5.0 years ago by kuragari.ch20

Take into account that the package will generate a file with the SNPs that contains information from the AllelikPeaks, so you will get from 200K to 300K snips instead of the 750K from the origin.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by kuragari.ch20
0
gravatar for sam
4.2 years ago by
sam0
Greece
sam0 wrote:

Hi Mangales, I am also currently working on CytoScan HD array data in my project. Did you find a solution? 

 

ADD COMMENTlink written 4.2 years ago by sam0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 770 users visited in the last hour