Hello, there,

I am testing the function "makeCountsFromAbundance" using the following data (numbers derived from Salmon output):

> count
   a  b  c  d
A 27 50 67 36
B  0  0  0  0
> length
        a       b       c       d
A  310.08  395.79  504.53  342.48
B 1026.00 1008.00 1009.00 1021.00
> abundance
     [,1] [,2] [,3] [,4]
[1,] 3.14 4.95 3.84 4.91
[2,] 0.00 0.00 0.00 0.00
>  f=makeCountsFromAbundance(count,abundance,length,countsFromAbundance="scaledTPM")                               
> f
   a  b  c  d
A 27 50 67 36
B  0  0  0  0

I don't think I got the "scaledTPM" as the documentation indicated... Instead, the output is just raw counts. Could anyone help me with it?

Thanks.

C.

The problem is just that this data is artificial (one gene). Try on real data.

You are testing using an edge case, where you only have two genes, and one has no observations (which isn't a real expectation). A more reasonable test would be to use two genes with actual observations:

> count
     [,1] [,2] [,3] [,4]
[1,]   27   50   67   36
[2,]    0    0    0    0
> count2 <- count
> count2[2,] <- c(1,2,4,3)
> count2
     [,1] [,2] [,3] [,4]
[1,]   27   50   67   36
[2,]    1    2    4    3
> abundance
     [,1] [,2] [,3] [,4]
[1,] 3.14 4.95 3.84 4.91
[2,] 0.00 0.00 0.00 0.00
> abundance2 <- abundance
> abundance2[2,] <- c(0.3,0.5, 0.7, 0.6)
> abundance2
     [,1] [,2] [,3] [,4]
[1,] 3.14 4.95 3.84 4.91
[2,] 0.30 0.50 0.70 0.60
> makeCountsFromAbundance(count2, abundance2, length)
         [,1]      [,2]     [,3]      [,4]
[1,] 25.55814 47.229358 60.05286 34.753176
[2,]  2.44186  4.770642 10.94714  4.246824