I have three Samples (replicates) per Group. I want to use a T-test to compare values (MappedReadsCPM) between groups. However, I have 4000 values to compare sequentially (designated by PeakNumber).
The following line is close, but it isn’t telling R to compare only peak\_1, and then only peak\_2, etc.

```
    t.test(MappedReadsCPM~Group, data=subset(data2, Group %in% c("1", "2")))$p.value

```

I don’t want to print the 4000 p-values - ideally I can add them to a dataframe.

```
    pvalues <- t.test(MappedReadsCPM~Group, data=subset(data2, Group %in% c("1", "2")))$p.value

```

data2

```
PeakNumber Sample   Group   MappedReadsCPM
peak_1  A   1   43.53819
peak_2  A   1   49.20722
peak_3  A   1   38.54943
peak_4  A   1   99.09472
peak_1  B   2   105.21728
peak_2  B   2   42.63114
peak_3  B   2   78.00591
peak_4  B   2   74.37773
peak_1  C   2   509.30606
peak_2  C   2   101.36234
peak_3  C   2   25.17051
peak_4  C   2   32.8804
peak_1  D   1   35.37478
peak_2  D   1   89.11722
peak_3  D   1   112.24688
peak_4  D   1   386.40139
peak_1  E   3   631.07692
peak_2  E   3   162.58791
peak_3  E   3   46.93961
peak_4  E   3   56.69035
peak_1  F   2   38.7762
peak_2  F   2   261.45587
peak_3  F   2   43.99171
peak_4  F   2   72.11012
peak_1  G   1   118.5962
peak_2  G   1   250.1178
peak_3  G   1   84.35
peak_4  G   1   386.40139

```