This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is It Possible To Convert Illumina Genotype Data Into Affymetrix-Like Format?

I realized that there are many tools only support Affymetrix SNP array data analysis. Is there any way or is it reliable to convert illumina SNP array data to Affymetrixl-like format?

For example, HAPSEG and ABSOLUTE developed by Broad institute (http://www.broadinstitute.org/cancer/cga/absolute_run), which are tools to analyze tumor purity/ploidy, only support Affy SNP 6.0 and 250K array. Does that mean there's definitely no clue to analyze illumina SNP array data at hand? Would really appreciate any suggestions, thanks.

illumina affymetrix
• 4,173 views • link
updated by Ram Ram • written by Conan • Conan

1 answer

If you want to estimate the tumor purity/cellularity you can use qpure for that. Qpure is based on illumuna snp-arrays. You need tumor and matched blood snp-arrays...

• 0 views • link
written by Irsan Irsan

Thank you for your instant reply. Yes I have paired sample and actually I did use several software: qpure, oncoSNP, ASCAT. As far as I understand qpure only estimates tumor purity but not ploidy. The latter two software showed me quite different results of purity and ploidy estimation, moreover in the ABSOLUTE paper author pointed out that has an apparent bias to underestimate the cancer cell fraction. So I wanna have a try with ABSOLUTE. It's disappointing that ABSOLUTE doesn't support illumina SNP arrays.

• 0 views • link
written by Conan • Conan

It seems like you are well informed ;-) if you want to run ABSOLUTE you need to segment your data first. On the website of absolute they talk about hapseg but the golden standard for tumor copy number segmentation is DNAcopy.

• 0 views • link
written by Irsan Irsan

This is a very old thread, but maybe you could share your experiences. I am having the same problem (ASCAT and OncoSNP give me quite different results for some samples) and wonder if ABSOLUTE gave you better results.

• 0 views • link
written by Pascal Pascal

Log in to answer this question.

More posts like this