[BioC] pd.hugene.1.0.st.v1

Mark Robinson mrobinson at wehi.EDU.AU
Fri Jul 31 06:48:18 CEST 2009

Hi all.

I wonder if its makes more sense to have the *transcript* version of  
this package, instead of the *probeset* version available when you  
install via:


It seems like as a default, more people would want gene-level  
summaries for these arrays ... especially since ~200k (~80%) of the  
probesets have 3 probes or less.

Of course I (and everyone around the world) could build this package  
locally from scratch using the transcript CSV, but it seems like there  
would be enough demand for this to make available direct from BioC.   
Just a thought.  Does anyone agree?

Or, am I missing something that will allow me to do gene-level  
analysis from this package?

My session is below.

Thanks in advance.

mac1618:Desktop mrobinson$ wc -l HuGene-1_0-st-v1.na29.*.csv
   257449 HuGene-1_0-st-v1.na29.hg18.probeset.csv
    33317 HuGene-1_0-st-v1.na29.hg18.transcript.csv

 > library(oligo)
Loading required package: oligoClasses
Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: preprocessCore
Welcome to oligo version 1.8.1
 > cf <- dir(celPath,"CEL")
 > fs <- read.celfiles( file.path(celPath,cf) )
Loading required package: pd.hugene.1.0.st.v1
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : rawData/cell_line/HuGene-1_0-st-v1//cancer1.CEL
Reading in : rawData/cell_line/HuGene-1_0-st-v1//cancer2.CEL
Reading in : rawData/cell_line/HuGene-1_0-st-v1//normal1.CEL
Reading in : rawData/cell_line/HuGene-1_0-st-v1//normal2.CEL
 > rmaOligo <- oligo::rma(fs)
Background correcting
Calculating Expression
dmOligo <- exprs(rmaOligo)
 > dmOligo <- exprs(rmaOligo)
 > dim(rmaOligo)
Features  Samples
   253002        4
 > sessionInfo()
R version 2.9.0 (2009-04-17)


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

other attached packages:
[1] pd.hugene.1.0.st.v1_2.4.1 RSQLite_0.7-1
[3] DBI_0.2-4                 oligo_1.8.1
[5] preprocessCore_1.6.0      oligoClasses_1.6.0
[7] Biobase_2.4.1

loaded via a namespace (and not attached):
[1] affxparser_1.15.6 affyio_1.12.0     Biostrings_2.12.1 IRanges_1.2.2
[5] splines_2.9.0

Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852

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