[BioC] normalisation + sam

[Wolfgang Huber]

Wolfgang Huber wrote

> Also, your fData(immgen) is ill-formatted. It should be a data.frame 
> with as many rows as features, instead it has as many columns, with one 
> row:
>  > dim(immgen)
> Features  Samples
>    23532      128
>  > dim(fData(immgen))
> [1] 23532     1


For the record....: It is ill-formatted, but in a different way:

 > str(fData(immgen))
'data.frame':	23532 obs. of  1 variable:
  $ symbol:List of 23532
   ..$ 10344622: chr "Gm6123"
   ..$ 10344624: chr "Lypla1"
   ..$ 10344633: chr "Tcea1"
   ..$ 10344637: chr "Atp6v1h"

I.e. "symbol" is a list of 23532 character vectors of length 1 each, 
while it should be a single character vectors of length 23532 (you 
probably used an 'lapply' somewhere an 'sapply' would have been better).

This is probably a tangential problem, not sure it has anything to do 
with those 'batch effects' in your data.


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber