Thanks a lot for the help, I will see the vignette and try to analyze my
data with these packages.

Claudia


On Sun, Nov 3, 2013 at 11:26 PM, Vincent Carey
<stvjc@channing.harvard.edu>wrote:

> with bioconductor these arrays can be processed with oligo (please see the
> vignette) and annotation comes from pd.* packages
>
> http://www.bioconductor.org/packages/release/bioc/html/oligo.html
>
>
> http://www.bioconductor.org/packages/release/data/annotation/html/pd.hugene.1.0.st.v1.html
>
> you may also consider xps
>
> http://www.bioconductor.org/packages/release/bioc/html/xps.html
>
>
> On Sun, Nov 3, 2013 at 4:15 PM, Claudia [guest] <guest@bioconductor.org>wrote:
>
>>
>> Hello,
>>
>> I'm trying to analyze some array data with Bioconductor and I receive the
>> following errore when I try to filter with GeneFilter: Error: getAnnMap:
>> package hugene10stv1 not available.
>>
>> This is the script I'm currently using:
>> setwd("C:/raw")
>> library(affy)
>> library("genefilter")
>> mydata <- ReadAffy()
>> pData(mydata)<-read.table("phenodata.txt", header=T,
>> row.names=1, sep="\t")
>> eset <- rma(mydata)
>> esetf<-nsFilter(eset)
>>
>> Annotation is hugene10stv1. I have already installed hugene10stv1cdf and
>> hugene10stv1probe packages but I receive the same error every time I try to
>> filter my set.
>>
>> Any help would be very much appreciated.
>>
>> Thanks a lot
>> Claudia
>>
>>  -- output of sessionInfo():
>>
>> > sessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: i386-w64-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252
>> [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
>> [5] LC_TIME=Italian_Italy.1252
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] hugene10stv1cdf_2.13.0 AnnotationDbi_1.24.0   genefilter_1.44.0
>> [4] affy_1.40.0            Biobase_2.22.0         BiocGenerics_0.8.0
>>
>> loaded via a namespace (and not attached):
>>  [1] affyio_1.30.0         annotate_1.40.0       BiocInstaller_1.12.0
>>  [4] DBI_0.2-7             IRanges_1.20.4        preprocessCore_1.24.0
>>  [7] RSQLite_0.11.4        splines_3.0.2         stats4_3.0.2
>> [10] survival_2.37-4       tools_3.0.2           XML_3.98-1.1
>> [13] xtable_1.7-1          zlibbioc_1.8.0
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>

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