Analysis data with edgeR having some values missed

[paumarc]

Hello everybody!

I'm trying to analyse some pyrosequencing data that some colleges sent me. I could get all experiment replicas for each experimental condition. The problem is that for the different genes I can have a different number of replicas. Even more, in some cases some results are missing. I think i should refill those values with 0's or N/A. what should i do in those cases that i do not have value? Working with averages do not provides good statistics

example of data

HEK293-Nach A2 64.09 - 62.06 64.2 -
HEK293-Nach B2 69.97 - 69.3 71.36 -
HEK293-Nach B2 62.22 - 62.26 61.89 -
HEK293-Nach B3 71.59 - 71.64 68.18 -
HEK293-Nach B3 57.61 - 59.55 60.71 -
HEK293-Nach B4 58.39 - 60.47 58.35 -
HEK293-Nach B4 66.21 - 65.46 66.13 -
HEK293-Nach B5 54.93 - 57.03 57.47 -
HEK293-Nach B5 61.58 - 66.07 65.93 -
HEK293-Nach B6 50 - 56.69 55.01 -
HEK293-Nach B6 58.57 - 65.68 63.94 -
HEK293 K 45.1 46.4 42.15 1.9 41.37
HEK293 K 45.92 44.88 42.2 1.74 41.16
HEK293 K 62.49 67.06 59.34 2.35 58.34
HEK293 K 59.21 67.21 58.54 3.75 56.7