I'm trying to figure out how to compare differential gene expression between samples. I've gotten to the first steps of data visualization, and using R and ballgown, I can run plotTranscripts or plotMeans to see differences in expression between samples for a given gene.
However, when visualizing using boxplot or plot and then plotting my samples' FPKM or Cov values, I see basically the reverse of what I saw when using plotTranscripts or plotMeans?
plotTranscripts of samples for argS gene expression:
boxPlot of argS gene expression (FPKM) across samples, showing the reverse trend of what is seen above (lactic acid has higher expression, control has lower expression: