[BioC] RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene

[Benilton Carvalho]

my bad... that's a mod that never made it to the code... in the
meantime, can you please run the following bit once (which will set
probeNames and after which everything will be fine):

setMethod("probeNames", "GeneFeatureSet",
                  function(object, subset=NULL){
                    res <- dbGetQuery(db(object), "SELECT fsetid FROM
pmfeature")[[1]]
                    as.character(res)
                  })

b

On Mon, Mar 1, 2010 at 10:53 AM, Mikhail Pachkov <pachkov at gmail.com> wrote:
> On Mon, Mar 1, 2010 at 11:51 AM, Benilton Carvalho
> <beniltoncarvalho at gmail.com> wrote:
>> can you give me the results for sessionInfo()?
>
>  sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pd.hugene.1.0.st.v1_3.0.0 RSQLite_0.8-3
> [3] DBI_0.2-5                 oligo_1.10.2
> [5] preprocessCore_1.8.0      oligoClasses_1.8.0
> [7] Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.18.0  affyio_1.14.0      Biostrings_2.14.12 IRanges_1.4.11
> [5] splines_2.10.1     tools_2.10.1
>