Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
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12 weeks ago

Hi all,

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:

image: 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:

image: boxPlot of argS gene expression (FPKM) across samples, showing the reverse trend of what is seen above

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