Hi everyone, I currently have a count matrix of Rna-seq data. To be precise I have 200 Tumor samples and 300 Healthy . Of those 200 Tumor samples I have 59 unique ones and the other are just the same sample with an additional string ("t0" in case is the Rna-seq of patient at time 0 , "t1" in case of treatment at time 1 and same for the other times until time 10 ). The problem is that not all samples have 10 times, meaning that Sample1 could have time 0 to time 3 , Sample 2 could have time 0 to time 8 and so on. What I want to study is how rna-seq of this tumor changes over treatment time . So I ask , just in words, how would you manipulate the data in order to reach this goal? What I need is just an idea on how would you manipulate the data and which design because so far I only did Differential Expression and Differential Co-Expression between Conditions, never studied time treatment development.
Little example of data :
Rows = Gene1 Gene2 Gene3 .... GeneN
Cols = Sample1t0 Sample2t0 .... Sample1t1 Sample2t1..... Sample1t2 Sample2t2.... ....Sample1t10 Sample2t10