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Old 07-02-2015, 08:54 AM   #1
Tom2013
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Default pca in DESeq2

Hello,

I run successfuly using the following code in DESeq2:
plotPCA(rld, intgroup=c("population", "treatment"))

However, I would like to use ggplot2 to draw a nice PCA plot as showed in the vignette. I run the following code and encounter a problem:
data <- plotPCA(rld, intgroup=c("population", "treatment"), returnData=TRUE)

The error is that the "returnData=TRUE" was not used. Does anybody know how to fix it?

Thank you in advance.
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Old 07-02-2015, 12:46 PM   #2
blancha
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Check the version of DESeq2 that you're running?

packageVersion("DESeq2")

This argument appeared in DESeq2 1.5.27.
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Old 07-02-2015, 01:19 PM   #3
Tom2013
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Thank you for your answer.

> packageVersion("DESeq2")
[1] 1.4.5

It's 1.4.5, although I re-installed DESeq2 from Bioconductor yesterday.
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Old 07-02-2015, 01:41 PM   #4
blancha
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You should check your Bioconductor version then.
You may have to update R first to be able to use the latest Bioconductor version.
So, I would update R first, then Bioconductor, and finally DESeq2.
It's a bit of work, but DESeq2 has evolved quite a bit over the different versions.
It may actually be worth repeating the entire analysis with the latest version of DESeq2.

I do agree that it is a common source of frustration that you only get the latest version of the package corresponding to your Bioconductor version when you install a package.

Last edited by blancha; 07-02-2015 at 02:00 PM.
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Old 07-03-2015, 08:58 AM   #5
Tom2013
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Smile

Quote:
Originally Posted by blancha View Post
You should check your Bioconductor version then.
You may have to update R first to be able to use the latest Bioconductor version.
So, I would update R first, then Bioconductor, and finally DESeq2.
It's a bit of work, but DESeq2 has evolved quite a bit over the different versions.
It may actually be worth repeating the entire analysis with the latest version of DESeq2.

I do agree that it is a common source of frustration that you only get the latest version of the package corresponding to your Bioconductor version when you install a package.
After installed the latest R, I can install the latest DESeq2. The code works now.
Thank you very much for your help.
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