Error in creating a volcano plot in MATLAB
I'm not sure if nowadays matlab is still a good option for informatics. I would rather go for a R script to make a volcano plot. If you don't want to have fancy code but functional one, you can even make the foldchange calculations and log2 transformation in excel and just plot the log2 fold change in x axis and the -log10 transform of the p/q values on the y axis.
If you need it, I could provide one of my own scripts.



Update: here is the actual script:

#load data into the 'res' variable
res &lt;- read.table("genes.txt", header=TRUE)
head(res)

# Make a basic volcano plot with grey dots
with(res, plot(log2FoldChange, -log10(qvalue), pch=19, col="#4A4E4D", xlab="Log2 Fold Change", xlim=c(-8,8)))

# Add colored points: "indianred" if padj&lt;0.0001, orange of log2FC&gt;2, green if both)
with(subset(res, qvalue&lt;.0001 ), points(log2FoldChange, -log10(qvalue), pch=19, col="#17B090"))
with(subset(res, abs(log2FoldChange)&gt;2), points(log2FoldChange, -log10(qvalue), pch=19, col="#F89538"))
with(subset(res, qvalue&lt;.0001 &amp; abs(log2FoldChange)&gt;2), points(log2FoldChange, -log10(qvalue), pch=19, col="#FA6367"))