Question: DNA microarray data available from TCGA?
1
gravatar for thi.nguyenthanh
3.9 years ago by
Australia
thi.nguyenthanh10 wrote:

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 • 2.3k views
ADD COMMENTlink modified 3.2 years ago by fatima0 • written 3.9 years ago by thi.nguyenthanh10
1
gravatar for Sean Davis
3.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k 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 COMMENTlink modified 3.9 years ago • written 3.9 years ago by Sean Davis25k

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 REPLYlink written 2.2 years ago by h72ghorashi0
0
gravatar for fatima
3.2 years ago by
fatima0
United States
fatima0 wrote:

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 

ADD COMMENTlink written 3.2 years ago by fatima0

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 REPLYlink written 3.2 years ago by Chris Miller20k

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 REPLYlink written 3.2 years ago by fatima0

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 REPLYlink written 3.2 years ago by Sean Davis25k

 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 REPLYlink written 3.2 years ago by fatima0

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

ADD REPLYlink written 3.2 years ago by Sean Davis25k
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