Question

How to find CNV or CN state information from rawcopy output ?

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6.2 years ago

sofie_carolina ▴ 30

I have to do CNV analysis and find the CNVs present in .CEL file. I used rawcopy for this purpose which is r package widely used for CNV analysis as like CHAS. But, the output files contain the information of Allelic.Imbalance. How will I find CN state or no. of copies information ?

Is there any good tools for CNV analysis taking .CEL file as input ?

sequencing cnv microarray next-gen SNP • 2.7k views

ADD COMMENT • link updated 6.1 years ago by lynn_redman ▴ 10 • written 6.2 years ago by sofie_carolina ▴ 30

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Which microarray platform did you use?

ADD REPLY • link 6.2 years ago by Kevin Blighe 88k

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Cytoscan HD. In rawcopy output while predicting CNV, I got Allelic Imbalance frequency scores. Is there any method to convert this scores to log2ratio or CN state ?

ADD REPLY • link 6.1 years ago by sofie_carolina ▴ 30

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Affymetrix have proprietary software for processing the Cytoscan HD, no? Surely that outputs log2 ratio and/or CN state?

ADD REPLY • link 6.1 years ago by Kevin Blighe 88k

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I have used rawcopy R-package to analyze .CEL files for CNV analysis. Here, outputs generated which have allelic imbalance frequencies instead of CN state or log2ratio. How it is possible to convert allelic imbalance frequencies to CNState or log2ratio ? This is my doubt, Sir.

ADD REPLY • link 6.1 years ago by sofie_carolina ▴ 30

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The homepage ( http://rawcopy.org/ ) indicates that it can output log ratios. You may want to check the manual to ensure that you are running the program correctly.

ADD REPLY • link 6.1 years ago by Kevin Blighe 88k

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Yes, log ratios are mentioned but the output file doesn't has that information. In output, it generates allelic imbalance frequencies but no information for log2ratio/logratio. How it is possible to convert allelic imbalance frequencies to logratios .. ? This is my question.

ADD REPLY • link 6.1 years ago by sofie_carolina ▴ 30

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Can you paste an example (or examples) of what it has actually output?

ADD REPLY • link 6.1 years ago by Kevin Blighe 88k

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Can you please share your email. I will share you the details including examples. Thanks !

ADD REPLY • link 6.1 years ago by sofie_carolina ▴ 30

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Sorry, cannot do that. There is a Biostars Slack channel, though: biostar.slack.com: Chat for the biostars community

There, you can ask follow-up with this question

ADD REPLY • link 6.1 years ago by Kevin Blighe 88k

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Hello,

Related to the issue reported here, I obtain this output after running Rawcopy. To prepare the input to ASCAT (BAF.txt and LogR.txt), what should I do?

Just to include the probes with BAF in both files.
Use only the probes with BAF in the BAF file, but include all probes in the LogR.
Include all the probes. Just to cut the columns to create the ASCAT input files.

Data

Thanks in advance.

ADD REPLY • link 5.9 years ago by sonia.zumalave • 0

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You may want to opena new question specific for ASCAT. Also, have you checked the manual for ASCAT?

ADD REPLY • link 5.9 years ago by Kevin Blighe 88k

score 1 · Answer 1 · 2018-10-29

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6.1 years ago

lynn_redman ▴ 10

I think the log ratios are reported in the column labeled "Values" under the segments.txt file. But I agree this package is poorly documented. I am trying to use the segments files generated from this for downstream analysis using GISTIC but I want to make sure this is the correct data first. I have emailed the author of the package.