hi Dimitra,

Please always include the output of sessionInfo(), so that we know what
versions of packages you are using.

I'm adding one of the ReportingTools authors. He might have a better answer
for what can be done in the current release.

Side note: we have been discussing how to handle the tradeoff better in the
next release, and from the DESeq2 side, we have created a simple class
'DESeqResults' for the object returned by results(). This way other package
authors can write methods for this object, so that all the arguments of the
results() function are accessible.

Mike


On Wed, Jan 22, 2014 at 6:29 AM, Dimitra Alexopoulou <
dimitra.alexopoulou@biotec.tu-dresden.de> wrote:

> Dear all,
>
> I've been happily using ReportingTools to publish an html report of my
> DESeq2 results so far having only two conditions to compare (i.e. WT to KO).
> I now have one Ctrl condition and three different mutations (say Mut1,
> Mut2 and Mut3):
>
> levels(condition) # my 4 different conditions
> # [1] "Ctrl"  "Mut1" "Mut2" "Mut3"
>
> dds # my DESeqDataset, including the results
> # class: DESeqDataSet
> # dim: 24791 12
> # exptData(0):
> # assays(3): counts mu cooks
> # rownames(24791): ENSMUSG00000000001 ENSMUSG00000000028 ...
> ENSMUSG00000093778 ENSMUSG00000093789
> # rowData metadata column names(31): baseMean baseVar ... deviance maxCooks
> # colnames(12): Ctrl_1 Ctrl_2 ... Mut3_2 Mut3_3
> # colData names(2): condition sizeFactor
>
> resultsNames(dds) # the results I have from DESeq2 saved in the dds
> # [1] "Intercept"               "condition_Mut1_vs_Ctrl"
> "condition_Mut2_vs_Ctrl" "condition_Mut3_vs_Ctrl"
>
>
> When I want to create the html report of the DESeq2 results obtained, I do
> the following:
>
> # Creating the html report using ReportingTools:
> desReport <- HTMLReport(shortName = "Blah_over_Ctrl_DEGs",
>                         title = 'Blah detailed results',
>                         basePath = myOutdir,
>                         reportDirectory = "./DEreports"
>                         )
> publish(dds, desReport, pvalueCutoff=0.1, factor = colData(dds)$condition)
> finish(desReport)
>
> The above returns by default results for the last coefficient from
> resultsNames, in my case: "condition_Mut3_vs_Ctrl".
>
> Is there a way to by-pass this default behaviour and output either:
> a. all results in one report, or
> b. each one of the results in a separate report, specifying this somehow
> to publish(), e.g.:
> publish(dds,name="condition_Mut2_vs_Ctrl", desReport, pvalueCutoff=0.1,
> factor=colData(dds)$condition)
> Or do I need to create a new dds_Mut2_over_Ctrl, subsetting the initial
> dds (which I don't know how to do and this would be my next question,
> especially to the DESeq2 people).
> I would like to avoid breaking the analysis into 3 comparisons from the
> beginning (meaning constructing 3 different DESeqDataSets and running the
> differential expression analysis on them).
>
> Thanks in advance,
> Dimitra
>
> --
> Dimitra Alexopoulou, PhD
> Deep Sequencing Group - SFB655
> Affiliation:
> DFG Research Center for Regenerative Therapies (CRTD)
> Biotechnology Center (Biotec)
> Technische Universität Dresden
>
> postal address:
> Deep Sequencing Group - SFB655
> c/o
> DFG-Center for Regenerative Therapies Dresden
> Cluster of Excellence / TU Dresden
> Fetscherstraße 105
> 01307 Dresden
>
> Phone: +49 (351) 458 82362
> Email: dimitraa(at)biotec.tu-dresden.de
> Web: http://www.biotec.tu-dresden.de/
>
> we are supported by:
> SFB 655, CRTD, Biotec, EU FP7, EFRE
>
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