[BioC] Human Gene ST using oligo package

Thu May 20 18:35:58 CEST 2010

while I figure out what solution to implement, I'd suggest using
something along the lines of:

pms = log2(pm(OligoRaw))
dens = oligo:::matDensity(pms)
cols = darkColors(ncol(pms))

boxplot(as.data.frame(pms), range=0, col=cols)
matplot(dens[["x"]], dens[["y"]], type="l", lwd=2, col=cols,
xlab="log-intensity", ylab="density")


b

On Thu, May 20, 2010 at 4:36 PM, Mike Smith <grimbough at googlemail.com> wrote:
> Hi Javier,
>
> You can get a boxplot of the geneFeatureSet and expression set objects
> using:
>
> boxplot(log2(exprs(OligoRaw))) and boxplot(exprs(OligoEset)) respectively.
>
> If I do the first command without the log transformation it takes about
> 10 minutes to plot for some reason, but it does still work.
>
> Mike Smith
>
>
> Javier Pérez Florido wrote:
>>
>> Dear Benilton,
>> Thanks again for your help. Detaching 'affy' makes it work.
>> However, I'm trying to use boxplot and histogram. For raw data it says:
>>
>> > boxplot(OligoRaw)
>> Error in validObject(.Object) :
>>  invalid class "ExpressionSet" object: featureNames differ between
>> assayData and featureData
>> Error in exprs(channel(eset, chns[i])) :
>>  error in evaluating the argument 'object' in selecting a method for
>> function 'exprs'
>>
>> And for an expression set object:
>>
>> > boxplot(OligoEset)
>> Error in .local(x, ...) : object 'nsamples' not found
>>
>> Do I have to detach any other package?
>>
>> Thanks again,
>> Javier
>>
>>
>> > sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
>>  LC_MONETARY=Spanish_Spain.1252
>> [4] LC_NUMERIC=C                   LC_TIME=Spanish_Spain.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1
>>     AnnotationDbi_1.10.0
>>  [4] limma_3.4.0                          vsn_3.16.0
>>     genefilter_1.30.0
>>  [7] pd.hugene.1.0.st.v1_3.0.1            RSQLite_0.8-4
>>      DBI_0.2-5
>> [10] oligo_1.12.0                         oligoClasses_1.10.0
>>      Biobase_2.8.0
>>
>> loaded via a namespace (and not attached):
>>  [1] affxparser_1.20.0     affy_1.26.0           affyio_1.16.0
>> annotate_1.26.0       Biostrings_2.16.0
>>  [6] grid_2.11.0           IRanges_1.6.0         lattice_0.18-5
>>  preprocessCore_1.10.0 splines_2.11.0
>> [11] survival_2.35-8       tools_2.11.0          xtable_1.5-6
>> >
>>
>>
>> On 19/05/2010 21:56, Benilton Carvalho wrote:
>>>
>>> detach affy and try again (when you loaded 'affy' you got a message
>>> saying that oligo::probeNames was being masked).
>>>
>>> fyi: we do have ideas on how to solve this.
>>>
>>> b
>>>
>>> 2010/5/19 Javier Pérez Florido<jpflorido at gmail.com>:
>>>
>>>>
>>>> Dear list,
>>>> Some time ago I used the oligo package to read and pre-process (rma) a
>>>> set
>>>> of Human Gene ST 1.0 CEL files and it was OK.
>>>>
>>>> Now, I have resumed my work and with the new version of oligo and R
>>>> (below
>>>> is my session info), the same code doesn't work (the new oligo vignette
>>>> is
>>>> quite different to the one I used before). I have downloaded first the
>>>> pd.hugene.1.0.st package from bioconductor and then I built it myself
>>>> (to
>>>> check if it was a problem of the annotation package) and the same error
>>>> appears:
>>>>
>>>> OligoRaw<-read.celfiles(filenames=list.celfiles())
>>>> OligoEset<-rma(OligoRaw,target="core") # It is a GeneFeatureSet object
>>>> Error in function (classes, fdef, mtable)  :
>>>>  unable to find an inherited method for function "probeNames", for
>>>> signature
>>>> "GeneFeatureSet"
>>>>
>>>> Any suggestions?
>>>> Thanks,
>>>> Javier
>>>>
>>>>
>>>> R version 2.11.0 (2010-04-22)
>>>> i386-pc-mingw32
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
>>>>  LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
>>>> [5] LC_TIME=Spanish_Spain.1252
>>>>
>>>> attached base packages:
>>>>  [1] grid      tools     tcltk     stats     graphics  grDevices utils
>>>> datasets  methods   base
>>>>
>>>> other attached packages:
>>>>  [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1
>>>>   RColorBrewer_1.0-2
>>>>  [4] gplots_2.7.4                         caTools_1.10
>>>>   bitops_1.0-4.1
>>>>  [7] gdata_2.8.0                          gtools_2.6.2
>>>>   oneChannelGUI_1.14.2
>>>> [10] RaExExonProbesetLocation_1.0.0       MoExExonProbesetLocation_1.0.0
>>>>   HuExExonProbesetLocationHg19_0.0.2
>>>> [13] edgeR_1.6.2                          IRanges_1.6.0
>>>>    preprocessCore_1.10.0
>>>> [16] GOstats_2.14.0                       graph_1.26.0
>>>>   Category_2.14.0
>>>> [19] AnnotationDbi_1.10.0                 tkWidgets_1.26.0
>>>>   DynDoc_1.26.0
>>>> [22] widgetTools_1.26.0                   affylmGUI_1.22.0
>>>>   affyio_1.16.0
>>>> [25] affy_1.26.0                          limma_3.4.0
>>>>    pd.hugene.1.0.st.v1_0.0.1
>>>> [28] pdInfoBuilder_1.12.0                 oligo_1.12.0
>>>>   oligoClasses_1.10.0
>>>> [31] affxparser_1.20.0                    RSQLite_0.8-4
>>>>    DBI_0.2-5
>>>> [34] Biobase_2.8.0
>>>>
>>>> loaded via a namespace:
>>>>  [1] annotate_1.26.0   Biostrings_2.16.0 genefilter_1.30.0 GO.db_2.4.1
>>>> GSEABase_1.10.0   RBGL_1.24.0       splines_2.11.0
>>>>  [8] survival_2.35-8   XML_3.1-0         xtable_1.5-6
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
>>
>
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