[BioC] removal of outliers in matrix

[Johannes Hanson]

Dear all,

After some work with analysis of micro array data I am now facing my first
metabolomics dataset. 
The first problem I encountered is that the structure of the data is
different from what I am used to. Due to the alignment of the chromatogram I
do have extreme outliers within the dataset. The alignment is good (and I
don't want to manually adjust 8000 peaks). If I could easily remove the
outliers the rest of the analysis would be easier. 
The outliers I want to remove are most often a total lack of signal as the
peak is missing. I do have five replicates of each treatment I am looking
for something that could remove only the extreme outliers (sample nr nine in
the example below). 

A typical outlier:
Untreated
0.00040016	0.001029071	0.00101226	0.000739958	0.000288475 
Treated
5.58151787	4.146639291	4.080655391	0.00120032	4.786810001

The data is structured as a matrix with one line per peak and the replicates
as individual columns (much like micro array data). 

Thanks for any suggestions on how to continue

Johannes