Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format

Hi everyone,

I am looking for a tool to convert Affy OncoScan format files into Affy SNP6.0 files. Affy 6.0 SNP array file is a cumulative file of LogR for all samples whereas Affy OncoScan provide individual file for LogR for each sample. I believe it can be done with a code in any suitable programming language but the problem I'm facing is that each OncoScan sample has different probes and making a cumulative file for all probes would introduce a myriad of missing values across all samples..Any ideas would be much appreciated!

Cheers

r

• 2,577 views • link

updated 3.2 years ago by Ram

• written 12.8 years ago by Jason •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

microarray data analysis in R
written 2.7 years ago by bioinformbeginner •

I am following this code for analysis in R of GSE113873 and only getting a symbol mapping to probe only 10 genes and enterzid and …
analysing bismark.cov.gz files
written 3.1 years ago by adR

Hi all, I have 100 whole bisulfate sequenced samples and generated 100 bismark.cov.gz files following the Bismark pipeline. I want to do differential methylation analysis …
Explore CNV data from illumina Array
written 5.7 years ago by mel22

Hello, I have received out put from OncoArray illumina array of CNV data. The file is a .txt like this : Sample_ID Sample_1 Sample_2 Sample_3 …
Demultiplexing multiple amplicons from one fastq based on primer sequence
written 5.7 years ago by WhiteN8 •

Hi all, I have some fastq files that are already demultiplexed based on sample ID. I have separate fastq files for Read 1 and Read …
TCGA purity data
written 8.1 years ago by Folder40g

Hi I know that Cosmics offers a file with the purity for each tumor sample but no BAF or LogR, but I'm interested in running …
CWL: A relative path as input
written 9.2 years ago by kevin.o.oluoch

I have a Common Workflow Language script that takes a single sample file as input. I'd like to use it to run several files. I've …
Question about CNV analysis on tumors
written 9.3 years ago by test •

I'd like to do CNV analysis on tumor samples (frozen tissue) to detect large arm level CNV as well as focal LOH, amplification, homozygous deletion. …
Processing With Snp6 Cel Files Into Cn Segmentations
written 12.5 years ago by J.F.Jiang

<p>Hi all,</p> <p>I am facing a problem to obtain the segmentation files for probes in SNP 6.0 files, I mean to obtain the log2ratio for …
How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output
written 12.7 years ago by Jason •

<p>Hi, </p> <p>I have checked the whole aroma.affymetrix website but I can't seem to work out their tutorials on creating a tab-delimited text file from …
How To Understand The Value For The Affychip Of Genomewidesnp_6?
written 13.1 years ago by jlshi.nudt

<p>I've download a dataset generated by Affymetrix Genome-Wide Human SNP 6.0 Array. I don't understand the means of numbers in series matrix files. The head …