DNA microarray data available from TCGA?

Question: DNA microarray data available from TCGA?

4.2 years ago by

Australia

I am new to TCGA. Can we download DNA microarray data from TCGA? I mean the DNA microarray data not the RNA-seq count data. Thanks.

gene • 2.5k views

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modified 3.6 years ago by fatima • 0 • written 4.2 years ago by thi.nguyenthanh • 10

4.2 years ago by

Sean Davis ♦ 25k

National Institutes of Health, Bethesda, MD

Sean Davis ♦ 25k wrote:

The TCGA data are available here:

https://tcga-data.nci.nih.gov/

Each project has potentially different platforms for microarrays (and some no microarrays at all).

ADD COMMENT • link modified 4.2 years ago • written 4.2 years ago by Sean Davis ♦ 25k

How can I understand if a project has a platform for microarrays? I'm new to TCGA and microarray too and I need to find DNA microarray dataset for colorectal cancer.

Thanks :)

ADD REPLY • link written 2.5 years ago by h72ghorashi • 0

3.6 years ago by

fatima • 0

United States

fatima • 0 wrote:

I am working with CODA gene expretion data from TCGA and I want CEL formt file but each zip file have text format and I dont know compatable with R or not !

tnx

ADD COMMENT • link written 3.6 years ago by fatima • 0

R can read in any sort of text file. Whether it's compatible with the particular package you want to use is another question. Much of bioinformatics involves massaging data formats to work with the tools that you want to use.

ADD REPLY • link written 3.6 years ago by Chris Miller ♦ 21k

tnx for your help i want • Convert the Affymetrix data to a format that can be used by the “createTissueSpecific()” Cobra Toolbox function so I need CEL format

ADD REPLY • link written 3.6 years ago by fatima • 0

Please see the link that I posted as an answer to this question. If you follow a couple of links, you'll end up here:

https://tcga-data.nci.nih.gov/tcga/dataAccessMatrix.htm

Choose the 133A array type under platform. Choose Level 1 data. Then, submit. That will allow you to create an archive with all the hgu-133a array data available.

ADD REPLY • link written 3.6 years ago by Sean Davis ♦ 25k

Thanks for your attention But I am working on COAD so it scale dont have 133A and I chose leve 1 and expression gene and output is unc_agilentg4502a_07 so i want convert it to a format that can be used by the “createTissueSpecific()” Cobra Toolbox function

ADD REPLY • link written 3.6 years ago by fatima • 0

Just to help everyone keep everything straight, please ask a new question about using Cobra Toolbox.

ADD REPLY • link written 3.6 years ago by Sean Davis ♦ 25k

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