**830**wrote:

Hi everybody, I have the counts (obtained by HTSeq) for a lot of genes(~58,000) at different time points (replicates).

```
gene t1_S1 t1_S2
ENSG00000000003.14 0 0
ENSG00000000005.5 0 0
ENSG00000000419.12 1 3
[...]
```

I woul like to calculate the correlation between the counts over each gene at the same timepoint to understand how reproducible the replication timing and progression is for each repeat. Any suggestions?

**9.0k**• written 20 months ago by Lila M •

**830**

Check out the

`cor`

function in R. Different kinds of correlation measures are available, including Spearman and Pearson.39kThis is what I am doing, but as I have a huge number of genes, R gets stuck . This is what I'm trying:

any other suggestion?

830Do I understand correctly that you aim to calculate 58000 correlation coefficients?

39kRead count correlation between samples

31k