edger and ccle

hibari

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Join Date: Sep 2016

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edger and ccle

09-28-2016, 03:10 AM

Hi all,

This is my first post here, so I am taking the opportunity to thank all the people who make this forum live.

It is possible to find read counts from CCLE here :

Office of Cancer Genomics

https://ocg.cancer.gov/ctd2-data-project/translational-genomics-research-institute-quantified-cancer-cell-line-encyclopedia

NCI's Office of Cancer Genomics (OCG) conducts structural, functional, and computational genomics research to improve patient diagnosis, treatments, and outcomes.

I would like to use these data to find genes involved in resistance to treatment.
I would like two group these cell lines in "sensitive" and "resistance" and test for the DEGs.
However there is no technical replicats for these data.

Let's say I have 32 cell lines in the "resistant" group and 32 cell lines in the "sensitive" group.
Can I perform a DEG analysis with edgeR ?
Can the 32 cell lines in each group be considered as replicats ?
Do you think my approach is valid ?

Thank you very much.
Tags: ccle, edger

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