Preprocessing
Bioconductor
Overview
• Data set Salmo, color flip design
Name Cy5 Cy3 FileName
2004012211 array1 self1 self2 2004012211.txt 2004012212 array2 self2 self1 2004012212.txt
RG$printer
$ngrid.r [1] 12
$ngrid.c [1] 4
$nspot.r [1] 17
$nspot.c [1] 17
Red background
Green background
Plot raw data
Raw data cartesian coordinates
Raw data log scale
Data background corrected
MA plot before normalisation
MA per print tip before normalisation
MA after print tip normalisation
MA after print tip normalisation
Box plot
Between array normalisation not essential
SWIRL DATASET
Between array
normalisation essential
Volcano plot
Log oddsL Log(p/(1-p))
SALMO array
• 6 replica’s (6 normalised ratios) Design
> Salmo.cl <-rep(c(1),6)
> Salmo.cl [1] 1 1 1 1 1 1 SAM
Paired,
SAM
SAM
CyberT
Results CyberT
Mn: mean ratio
# obs: number of ratios available to calculate the statistics SD: standard deviation on the ratio estimates
T, p calculated t and p value that indicate the significance of the measurement
Results CyberT
