Question: The Cancer Genome Atlas (TCGA) gene expression analysis
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gravatar for lovely.molbio
10 months ago by
lovely.molbio10 wrote:

Hi, I am trying to analyze TCGA breast cancer patients data. Based on a gene expression (high and low) and survival, I have divided all breast cancer patients into two groups. I have sorted patients/sample ID into two groups. Now, I want to analyze gene expression of whole set (high expression sample vs low expression samples) by creating two groups and analyzing DEG. Do i need to download the data from TCGA to perform this analysis? If yes, how can i do this? Thanks a lot in advance.

gene expression tcga • 558 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by lovely.molbio10

...but you indicate that you have already obtained the data, or am I incorrect? What exactly do you currently have, and what more do you need?

ADD REPLYlink written 10 months ago by Kevin Blighe60k

Thank you for your response. No, I have not downloaded any data from TCGA, yet. I have used Broad Firehose and some other tools to classify the data. Now I would like to perform a detailed gene expression analysis among two groups. There is normalized data available on Broad firehose portal, but, as much as I could understand this Broad Firehose data is not compatible with R based DEG analysis. So, my question is how should I proceed now from here?

ADD REPLYlink written 10 months ago by lovely.molbio10
1

I have not used the data from Broad Firehose; however, UCSC's Xena Browser has expression data available in HTseq and FPKM counts: https://xenabrowser.net/datapages/ (look for the 'GDC TCGA' datasets)

You will want those HTseq counts, however, you will have to convert them back to raw integer counts, as I show here: A: Normalisation of RNAseq data from UCSC Xena Browser

After that, the counts will be okay to input to DESeq2, EdgeR, or the limma / voom pipeline for processing.

ADD REPLYlink modified 10 months ago • written 10 months ago by Kevin Blighe60k
1

Awesome. I'll do that. Thanks a lot.

ADD REPLYlink written 10 months ago by lovely.molbio10
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