[BioC] GenomicAnnotationsFromdataframe error

[Maria [guest]]

Hi everybody!

I am analysing HumanExon arrays with the PREDA package. I have normalized my data and use the command statisticsForPREDAfromEset without problems but when I try to use the command GenomicAnnotationsFromdataframe an error always appears.

The commands I have written are the following: 
> library(PREDA)
> infofile<-"mycells4.txt"
> sampleinfo<-read.table(infofile, sep="\t", header=TRUE)
> head(sampleinfo)
                                         Array Sample.Name Probe
1     GSM472906_X_Hs_HEPG_E_080131_02_DS7764_D     HepG2_1     1
2     GSM472907_X_Hs_HEPG_E_080602_01_DS7768_W     HepG2_2     1
3 GSM510514_X_Hs_HRPEpiC_E_091208_11_DS12583_W      RPE1_1     2
4 GSM510515_X_Hs_HRPEpiC_E_091211_03_DS12568_W      RPE1_2     2
> GEstatisticsForPREDA<-statisticsForPREDAfromEset(ppData, statisticType="tstatistic", referenceGroupLabel="1", classVector=sampleinfo[,"Probe"])
> GEGenomicAnnotations<-eset2GenomicAnnotations(ppData, retain.chrs=1:22)
Loading required package: pd.huex.1.0.st.v2.db
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pd.huex.1.0.st.v2.db’
Error in mget(x, envir = getAnnMap(what, chip = data, load = load), ifnotfound = NA) : 
  error in evaluating the argument 'envir' in selecting a method for function 'mget': Error: getAnnMap: pd.huex.1.0.st.v2.db package not attached and load is FALSE
> infofile2<-"Data2.txt"
> sampleinfo2<-read.table(infofile2,sep="\t",header=TRUE)
> colnames(sampleinfo2)
sampleinfo3<-as.data.frame(sampleinfo2)
> CNGenomicsAnnotations<-GenomicAnnotationsFromdataframe(sampleinfo3,ids_column="Constitutive_IDs_used",chr_column="Chromosome",strand_column="Strand",chromosomesLabelsInput=1:22,MinusStrandString="-",PlusStrandString="+")
Error in .local(.Object, ...) : 
  (list) object cannot be coerced to type 'double'
In addition: Warning messages:
1: In `[<-.factor`(`*tmp*`, iseq, value = c(-1, -1, -1, -1, -1, -1,  :
  invalid factor level, NAs generated
2: In `[<-.factor`(`*tmp*`, iseq, value = c(1, 1, 1, 1, 1, 1, 1, 1,  :
  invalid factor level, NAs generated

I am pretty sure that I have created a data frame from my data.

Any suggestion?

Thank you.

Best

Maria

 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] PREDA_1.4.0             annotate_1.36.0         AnnotationDbi_1.20.7    multtest_2.14.0        
 [5] lokern_1.1-3            pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.2          DBI_0.2-5              
 [9] oligo_1.22.0            Biobase_2.18.0          oligoClasses_1.20.0     BiocGenerics_0.4.0     

loaded via a namespace (and not attached):
 [1] affxparser_1.30.2     affyio_1.26.0         BiocInstaller_1.8.3   Biostrings_2.26.3     bit_1.1-10           
 [6] codetools_0.2-8       ff_2.2-11             foreach_1.4.0         GenomicRanges_1.10.7  IRanges_1.16.6       
[11] iterators_1.0.6       MASS_7.3-23           parallel_2.15.3       preprocessCore_1.20.0 sfsmisc_1.0-23       
[16] splines_2.15.3        stats4_2.15.3         survival_2.37-4       XML_3.96-1.1          xtable_1.7-1         
[21] zlibbioc_1.4.0       


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