Thank you very much for your response. You already did a lot of for me.
A column missed, it is the pvalue (table test).
I obtain a graph but with the pvalue missing, I don't know if it is correct.
Here, is a code in R.
Generate a plot of log fold change versus mean expression (MA plot)
## S4 method for signature 'data.frame'
plotMA( object, ylim = NULL,
colNonSig = "gray32", colSig = "red3", colLine = "#ff000080",
log = "x", cex=0.45, xlab="mean expression", ylab="log fold change", ... )
Arguments
object
A data.frame with (at least) three columns, the first containing the mean expression values (for the x-axis), the second the logarithmic fold change (for the-y axis) and the third a logical vector indicating significance (for the colouring of the dots).
ylim
The limits for the y-axis. If missing, an attempt is made to choose a sensible value. Dots exceeding the limits will be displayed as triangles at the limits, pointing outwards.
colNonSig
colour to use for non-significant data points.
colSig
colour to use for significant data points.
colLine
colour to use for the horizontal (y=0) line.
log
which axis/axes should be logarithmic; will be passed to plot .
cex
The cex parameter for plot .
xlab
The x-axis label.
ylab
The y-axis label.
...
Further parameters to be passed through to plot .
... View more
