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-   -   Differential expression analysis using DESeq for TCGA data (http://seqanswers.com/forums/showthread.php?t=66005)

alrossi 02-02-2016 07:46 AM

Differential expression analysis using DESeq for TCGA data
 
Hi.

I’m analysing RNA Sequencing (RNAseq) data of Breast Invasive Carcinoma cases for tumor-normal matched samples downloaded from TCGA. An amount of 113 samples were retrieved. I’m interested in the matched tumor and normal samples to evaluate gene expression differences between invasive breast carcinoma tissue and its matched normal tissue.

I’m using with the raw_counts (...rsem.genes.result) as input of DESeq methods to perform differential expression analysis.

Should I use all genes raw counts as input of DESeq methods or I can use just the subset of genes I’m interested?

Here is the count read data: https://www.dropbox.com/s/niv6xk8bbp...GENES.csv?dl=0

Thank you.

André Rossi


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