[BioC] errors in FRMA

[Mayte Suarez-Farinas]

>annotation(object)
[1] "hgu133plus2"


>new.object<-convertPlatform(object,'hgu133a')
Loading required package: hgu133aprobe
Loading required package: hgu133plus2probe


Attaching package: ‘hgu133plus2cdf’

The following object(s) are masked from ‘package:hgu133acdf’:

    i2xy, xy2i

head(intensity(new.object))
   1  2  3  4  5  6  7  8  9 10
1 NA NA NA NA NA NA NA NA NA NA
2 NA NA NA NA NA NA NA NA NA NA
3 NA NA NA NA NA NA NA NA NA NA
4 NA NA NA NA NA NA NA NA NA NA
5 NA NA NA NA NA NA NA NA NA NA
6 NA NA NA NA NA NA NA NA NA NA



sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] frmaTools_1.6.0            preprocessCore_1.16.0      a4_1.2.0                   a4Reporting_1.2.0          a4Classif_1.2.0           
 [6] varSelRF_0.7-3             randomForest_4.6-6         pamr_1.54                  survival_2.36-12           ROCR_1.0-4                
[11] MLInterfaces_1.34.2        sfsmisc_1.0-19             cluster_1.14.2             rda_1.0.2                  rpart_3.1-52              
[16] a4Base_1.2.3               a4Core_1.2.0               a4Preproc_1.2.0            glmnet_1.7.3               Matrix_1.0-4              
[21] multtest_2.10.0            mpm_1.0-22                 MASS_7.3-17                annaffy_1.26.0             gplots_2.10.1             
[26] KernSmooth_2.23-7          caTools_1.12               bitops_1.0-4.1             gdata_2.8.2                gtools_2.6.2              
[31] limma_3.10.3               annotate_1.32.1            simpleaffy_2.30.0          genefilter_1.36.0          lattice_0.20-0            
[36] gcrma_2.26.0               arrayQualityMetrics_3.10.0 affycoretools_1.26.0       KEGG.db_2.6.1              GO.db_2.6.1               
[41] RSQLite_0.11.1             DBI_0.2-5                  AnnotationDbi_1.16.19      affy_1.32.1                Biobase_2.14.0            

loaded via a namespace (and not attached):
 [1] affyio_1.22.0       affyPLM_1.30.0      beadarray_2.4.2     BiocInstaller_1.2.1 biomaRt_2.10.0      Biostrings_2.22.0   Cairo_1.5-1        
 [8] Category_2.20.0     colorspace_1.1-1    GOstats_2.20.0      graph_1.32.0        GSEABase_1.16.1     Hmisc_3.9-2         hwriter_1.3        
[15] IRanges_1.12.6      latticeExtra_0.6-19 mboost_2.1-2        plyr_1.7.1          RBGL_1.30.1         RColorBrewer_1.0-5  RCurl_1.91-1       
[22] reshape2_1.2.1      setRNG_2009.11-1    stringr_0.6         SVGAnnotation_0.9-0 tools_2.14.1        vsn_3.22.0          XML_3.9-4          
[29] xtable_1.7-0        zlibbioc_1.0.1     



Mayte Suarez-Farinas
Research Assistant Professor,  Laboratory of Investigative Dermatology
Biostatistician,  Center for Clinical and Translational Science
The Rockefeller University 
1230 York Ave, Box 178,
New York, NY, 10065
Phone: +1(212) 327-8213
Fax:      +1(212) 327-8232










On Apr 28, 2012, at 3:55 PM, Matthew McCall wrote:

> sessionInfo