DNA microarray data available from TCGA?

Question

[thi.nguyenthanh]

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.

Answer 1

[Sean Davis]

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).

[h72ghorashi]

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 :)

Answer 2

[fatima]

Hi

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

[Chris Miller]

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.

[fatima]

Thanks for your help I want to Convert the Affymetrix data to a format that can be used by the "createTissueSpecific()" Cobra Toolbox function so I need CEL format

[Sean Davis]

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.

[fatima]

Thanks for your attention But I am working on COAD so it scale don't have 133A and I chose level 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

[Sean Davis]

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