I have a table like that :
a_25 a_26 a_27 a_28 a_29 a_30
ENST00000673902.1 26 38 40 38 36 63
ENST00000618500.4 0 0 0 0 0 0
ENST00000420646.6 0 26 0 115 0 220
ENST00000394991.8 3496 2272 4848 2508 2427 3024
ENST00000336904.7 19 0 40 43 61 0
ENST00000394989.6 0 0 27 0 0 40
ENST00000673766.1 220 274 321 338 248 304
ENST00000673718.1 56 197 603 176 437 43
ENST00000674129.1 743 538 1047 202 276 269
ENST00000345009.8 0 0 0 0 0 0
ENST00000394986.5 85 97 277 10 41 63
ENST00000508895.5 3034 2152 5165 1231 1245 1814
ENST00000506244.5 554 283 276 247 248 182
ENST00000505199.5 0 0 0 0 0 0
ENST00000611107.1 0 0 0 0 0 0
ENST00000502987.5 113 128 213 127 139 144
ENST00000506691.1 212 170 397 87 106 126
ENSRNOT00000039247 1623 1230 2239 1413 1573 1611
ENSRNOT00000118428 0 0 0 106 119 132
I would like first to normalize it and then perform a t-test for the two conditions I have the one con1 (samples a_25 a_26 a_27) and the second con2 (samples a_28 a_29 a_30). How to do it in R ?
I tried to normalize with cpm
Norm_count <- cpm(Counts,log10 = T)
But the result is strange big numbers ! What kind of normalization is proper and how to perform a t test for each ENST0000X lets say and export a value in R ?