I have expression values (log2) for 200 genes in two conditions treated and untreated and for each condition I have 20 replicates. The dataset looks like this:
Gene UT1 UT2 T1 T2 DDR1 8.111795978 7.7606511867 7.9362235824 7.5974674936 RFC2 10.2418824097 9.7752152714 10.0085488406 9.5723427524 HSPA6 6.5850239731 6.7916563534 6.6883401632 7.3659252344 PAX8 9.2965160827 9.2031177653 9.249816924 8.667772504 GUCA1A 5.4828021059 5.3797749957 5.4312885508 5.1297319374
I have shown only two replicates for each sample in the sample data.
How can I calculate similarity in gene expression for each gene in two conditions and rank them from highest to lowest (in terms of similarity)?
I am looking for a solution in R or python. The
cor function in R does not give me what i want.