Hi Michael,

here is my sessionInfo(), I realized I had forgotten it when I had 
already pressed the Send button, sorry :S

R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C LC_TIME=en_US.UTF-8        
LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8 
LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C 
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods   
base

other attached packages:
  [1] genefilter_1.44.0          biomaRt_2.18.0 *ReportingTools_2.2.0 * 
AnnotationDbi_1.24.0
  [5] RSQLite_0.11.4             DBI_0.2-7 knitr_1.5                  
vsn_3.30.0
  [9] Biobase_2.22.0             FactoMineR_1.25 
leaps_2.9                  scatterplot3d_0.3-34
[13] cluster_1.14.4             lattice_0.20-24 
ellipse_0.3-8              car_2.0-19
[17] PerformanceAnalytics_1.1.0 xts_0.9-7 zoo_1.7-10 *DESeq2_1.2.8*
[21] RcppArmadillo_0.3.920.3    Rcpp_0.10.6 GenomicRanges_1.14.3       
XVector_0.2.0
[25] IRanges_1.20.6             BiocGenerics_0.8.0 
gplots_2.12.1              plotrix_3.5-2
[29] scales_0.2.3               RColorBrewer_1.0-5 
reshape2_1.2.2             plyr_1.8

loaded via a namespace (and not attached):
  [1] affy_1.40.0             affyio_1.30.0 annotate_1.40.0         
AnnotationForge_1.4.4 BiocInstaller_1.12.0
  [6] Biostrings_2.30.1       biovizBase_1.10.5 bitops_1.0-6            
BSgenome_1.30.0 Category_2.28.0
[11] caTools_1.16            colorspace_1.2-4 dichromat_2.0-0         
digest_0.6.4 edgeR_3.4.2
[16] evaluate_0.5.1          formatR_0.10 Formula_1.1-1           
gdata_2.13.2 GenomicFeatures_1.14.2
[21] ggbio_1.10.10           ggplot2_0.9.3.1 GO.db_2.10.1            
GOstats_2.28.0 graph_1.40.0
[26] grid_3.0.2              gridExtra_0.9.1 GSEABase_1.24.0         
gtable_0.1.2 gtools_3.1.1
[31] Hmisc_3.13-0            hwriter_1.3 KernSmooth_2.23-10      
labeling_0.2 limma_3.18.5
[36] locfit_1.5-9.1          MASS_7.3-29 Matrix_1.1-1.1          
munsell_0.4.2 nnet_7.3-7
[41] PFAM.db_2.10.1          preprocessCore_1.24.0 
proto_0.3-10            RBGL_1.38.0 RCurl_1.95-4.1
[46] R.methodsS3_1.5.2       R.oo_1.15.8 Rsamtools_1.14.2        
rtracklayer_1.22.0 R.utils_1.28.4
[51] splines_3.0.2           stats4_3.0.2 stringr_0.6.2           
survival_2.37-4 tools_3.0.2
[56] VariantAnnotation_1.8.7 XML_3.98-1.1 xtable_1.7-1            
zlibbioc_1.8.0

On 01/22/2014 03:20 PM, Michael Love wrote:
> 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 
> <mailto: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 <tel:%2B49%20%28351%29%20458%2082362>
>     Email: dimitraa(at)biotec.tu-dresden.de <http://biotec.tu-dresden.de>
>     Web: http://www.biotec.tu-dresden.de/
>
>     we are supported by:
>     SFB 655, CRTD, Biotec, EU FP7, EFRE
>
>     _______________________________________________
>     Bioconductor mailing list
>     Bioconductor@r-project.org <mailto:Bioconductor@r-project.org>
>     https://stat.ethz.ch/mailman/listinfo/bioconductor
>     Search the archives:
>     http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
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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