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
