[BioC] limma barcodeplot with 2 groups

[Gordon K Smyth]

Dear Dario,

The "labels" of the barcodeplot give the names of the two groups you are 
comparing (cancer vs normal for example).  If you are comparing cancer vs 
normal so such positive t-statistics indicate up in cancer, then you would 
put the cancer label on the left and the normal label on the right.  The 
labels are the same for both gene sets, because the same groups are being 
compared in each case.  Hence the labels are at the ends of the plot.

I think that you have assumed that the labels are intended to be for the 
gene sets, which they are not.

Best wishes
Gordon

> Date: Fri, 10 Feb 2012 12:00:12 +1100 (EST)
> From: Dario Strbenac <D.Strbenac at garvan.org.au>
> To: bioconductor at r-project.org
> Subject: [BioC] limma barcodeplot with 2 groups
> Message-ID: <20120210120012.BQA38016 at gimr.garvan.unsw.edu.au>
> Content-Type: text/plain; charset="us-ascii"
>
> Hello,
>
> The labels that I get are still on the side, as for a 1-sample plot. 
> Would it make more sense graphically to have them at the top and botton 
> of the graphic for 2-sample plots ? In the current format, I cannot tell 
> which label relates to which colour.
>
> I have limma_3.10.2
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
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