This my first post here, so first I would like to thank active people on this forum because it was very helpful to me :)
Here we can find reads counts for 935 cancer cell lines : https://ocg.cancer.gov/ctd2-data-project/translational-genomics-research-institute-quantified-cancer-cell-line-encyclopedia There is just one reads counting for each cell line.
I took some of these cell lines and grouped them between "resistant" and "sensitive". Now I would like to run edgeR or DESeq2 for differential gene expression.
For example let's say I have 6 cell lines : A, B, C, D, E, and F, with their reads count. In the group "resistant", I have A, B and C. In the group "sensitive", I have C, D and E. I would to use DESeq2 or edgeR in order assess differentially expressed genes.
So in this configuration, their is no technical replicates, but the 3 different cell lines of each group are considered as replicates. Is that correst to do this ?
Thank you very much.