[Bioc-devel] EBSeq C1Mean and C2Mean Values

[Dario Strbenac]

Hello,

In the documentation, it is described as :

C1Mean        The mean of each transcript within Condition 1 (adjusted by normalization factors).

C2Mean        The mean of each transcript within Condition 2 (adjusted by normalization factors).

However, when I look at it :

> str(test32vs24$C1Mean)
List of 3
 $ : Named num [1:43503] 0.301 2.078 6.217 3.035 0.239 ...
  ..- attr(*, "names")= chr [1:43503] "comp10246_c0_seq1" "comp102905_c0_seq1" "comp10314_c0_seq1" "comp10323_c0_seq1" ...
 $ : Named num [1:28426] 2.99 1.62 2.61 0 0 ...
  ..- attr(*, "names")= chr [1:28426] "comp10084_c0_seq1" "comp10094_c0_seq1" "comp10154_c0_seq1" "comp10161_c0_seq1" ...
 $ : Named num [1:118329] 2385.71 419.68 2926.13 7.39 6.39 ...
  ..- attr(*, "names")= chr [1:118329] "comp139431_c0_seq1" "comp139431_c0_seq2" "comp139431_c0_seq3" "comp156500_c0_seq1" ...

Presumably, the data is split into the three lists because of NgVector. It would be better if it was returned as one vector, in the same order as the input data. That would make it consistent with how PostFC and GetPP functions return their data.

Hopefully in the future, there can be a topTable function, like in limma and edgeR, that puts all of these results nicely into a data frame.

--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia