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,i ds_column="Constitutive_IDs_used",chr_column="Chromosome",strand_colum n="Strand",chromosomesLabelsInput=1:22,MinusStrandString="-",PlusStran dString="+") 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 -- Sent via the guest posting facility at bioconductor.org.