Compare RNA-seq and qPCR results using bar plots with error bars

[aggp11]

Hi,

We performed RNA-Seq on 3 biological replicates each for Control vs. Treated libraries. We used DESeq and got a list of significant DE genes. We have performed RT-qPCR for a subset of these genes. Now I would like to compare the log2FC values between the 2 approaches. Is there a good way to look at this as a graph? I was thinking of making bar plots for the log2FC values, however I am stuck on the error bars for RNA-seq. I can use SD for error bars for the qPCR data, however what can I use for the RNA-seq data to get bar plots with error bars?

Any help will be appreciated.

Thanks

[dpryan]

At least with DESeq2, there's an lfcSE column (standard error of the log2 fold-change), which would be appropriate. For the actual graph, you can use ggplot2 and make an xy scatter plot with the appropriate error bars. There's an example of how that work here.