Hi ,

I have a question about averaging microarray probes of a given dataset. It seems like avereps of limma calculates the average for replicate probes. This is OK, as soon as the missing values are introduced the calculations of average are not accurate (see example below).

Thank you.

Toufiq

> Data
    Features Col1_Counts CSC1_Counts BC_Counts
1  Feature_1    6.643856    7.228819  5.643856
2  Feature_1    3.321928    5.643856  6.228819
3  Feature_1   10.965784    7.228819  6.643856
4  Feature_4          NA    1.584963  3.321928
5  Feature_5   10.965784    5.643856  6.228819
6  Feature_6          NA          NA        NA
7  Feature_6    3.459432    3.584963  3.700440
8  Feature_8    3.906891    4.000000  4.087463
9  Feature_9    4.247928    4.321928  4.392317
10 Feature_9          NA    4.523562        NA

> avereps(Data, ID=Data$Features)

     Features    Col1_Counts CSC1_Counts BC_Counts 
[1,] "Feature_1" " 6.643856" "7.228819"  "5.643856"
[2,] "Feature_4" NA          "1.584963"  "3.321928"
[3,] "Feature_5" "10.965784" "5.643856"  "6.228819"
[4,] "Feature_6" NA          NA          NA        
[5,] "Feature_8" " 3.906891" "4.000000"  "4.087463"
[6,] "Feature_9" " 4.247928" "4.321928"  "4.392317"