[Bioc-devel] Differential Analysis of Raw TCGA data using Bioconductor’s ExperimentHub

Sonali B Arora sarora at fredhutch.org
Thu Mar 31 20:01:11 CEST 2016

Hi Hamada,

Bioconductor has two branches - release and development. ExperimentHub 
has been added  to the devel branch of Bioconductor recently -and it 
will thus work only with the devel version of R until it is added to the 
release branch ( April 15th, 2016)
The release schedule can be found here:

You have two options right now , if you don't want to change your 
current R version -

a) ExperimentHub will be available in release version of Bioconductor 
after the upcoming release ( April 15th, 2016 ).
You can wait till April 15th - and retry then.

eh = ExperimentHub()
query(eh , "GSE62944")
tcga_data <- eh[["EH1"]]

b) AnnotationHub was the original place where the raw TCGA data was 
added ! and you can thus access GSE62944 from there using the same code.

ah = AnnotationHub()
query(ah , "GSE62944")
tcga_data = ah[["AH28855"]]
## follow rest of the Experiment Hub vignette.

I use R-devel -  here is my sessionInfo() for option(a)

 > sessionInfo()
R Under development (unstable) (2015-10-15 r69519)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
[1] Biobase_2.31.3       ExperimentHub_0.99.8 AnnotationHub_2.3.16
[4] BiocGenerics_0.17.3

loaded via a namespace (and not attached):
  [1] Rcpp_0.12.4                  IRanges_2.5.40
  [3] digest_0.6.9                 mime_0.4
  [5] R6_2.1.2                     xtable_1.8-2
  [7] DBI_0.3.1                    stats4_3.3.0
  [9] RSQLite_1.0.0                BiocInstaller_1.21.4
[11] httr_1.1.0                   curl_0.9.6
[13] S4Vectors_0.9.44             tools_3.3.0
[15] shiny_0.13.2                 httpuv_1.3.3
[17] AnnotationDbi_1.33.7         htmltools_0.3.5
[19] interactiveDisplayBase_1.9.0

Also, in the future, please cc the bioc-devel mailing list or ask this 
question on the support site (https://support.bioconductor.org/) so that 
other can also benefit from your questions.

Thanks and Regards,

On 3/31/2016 2:11 AM, AJMAL, HAMDA wrote:
> Dear Sonali,
> I am a PhD student from National University of Ireland, Galway. I am 
> trying to do differential analysis of TCGA available from GEO as 
> GSE62944. While searching for methods to load data into R, I came 
> across your post in 
> https://bioconductor.org/packages/devel/data/experiment/vignettes/GSE62944/inst/doc/GSE62944.html
> Would you be able to tell me which version of R you used? Can you tell 
> me your session info? Because for me, ExperimentHub package is 
> not install-able in latest version of R, i.e 3.2.4 (revised). Note 
> that I also tried 3.2.3 and 3.2.1. My OS is windows.
> Your help would be much appreciated.
> Regards,
> Hamda bint e Ajmal
> PhD Student
> Machine Learning and Data mining Group
> Discipline of IT, NUI Galway
> Phone:+353 83 1881575

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