Hello everyone,
I have RNA-seq data coming from control, breast cancer and endometrial cancer patients. Is an ongoing study and so far we've sequenced 15 patients (5 control, 5 breast cancer and 5 endometrial cancer) about a year ago and 5 patients (1 control, 2 breast cancer and 2 endometrial cancer) a month ago.
I want to compare between the independent batches and also combine them and do a global analysis. I did an independent DE analysis on each batch using EdgeR and DESeq2 however when i compare the gene lists I have very few common DE genes. Do I need to do some kind of normalisation before i compare them? About the global analysis, I will put everything together but how can I correct for batch effects?
Thank you so much!
I have RNA-seq data coming from control, breast cancer and endometrial cancer patients. Is an ongoing study and so far we've sequenced 15 patients (5 control, 5 breast cancer and 5 endometrial cancer) about a year ago and 5 patients (1 control, 2 breast cancer and 2 endometrial cancer) a month ago.
I want to compare between the independent batches and also combine them and do a global analysis. I did an independent DE analysis on each batch using EdgeR and DESeq2 however when i compare the gene lists I have very few common DE genes. Do I need to do some kind of normalisation before i compare them? About the global analysis, I will put everything together but how can I correct for batch effects?
Thank you so much!
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