Dario, you should really report these issues directly to the package
maintainer.  At least cc them on posts like this.

Kasper


On Thu, Jan 23, 2014 at 1:00 AM, Dario Strbenac
<dstr7320@uni.sydney.edu.au>wrote:

> 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
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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