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

[Benilton Carvalho]

bug fixed on 1.10.3, to appear online in about 24 hours.

b

On Mon, Mar 1, 2010 at 11:06 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> 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
>>
>