Hi, I have been trying to follow the Cold Spring Harbor tutorial with my own data. I'm stuck on the call to peaklist <- cmarrt.peak() call. Up to that point, everything seems to be working and making sense, including normalize.Probes and getRatio. I am using Sc03b_MR_v04.bpmap. Thanks in advance, Susan This works fine. > chrs [1] "Sc:Oct_2003;chr1" "Sc:Oct_2003;chr2" [3] "Sc:Oct_2003;chr3" "Sc:Oct_2003;chr4" [5] "Sc:Oct_2003;chr5" "Sc:Oct_2003;chr6" [7] "Sc:Oct_2003;chr7" "Sc:Oct_2003;chr8" [9] "Sc:Oct_2003;chr9" "Sc:Oct_2003;chr10" [11] "Sc:Oct_2003;chr11" "Sc:Oct_2003;chr12" [13] "Sc:Oct_2003;chr13" "Sc:Oct_2003;chr14" [15] "Sc:Oct_2003;chr15" "Sc:Oct_2003;chr16" [17] "Sc:Oct_2003;mitochondrion" > pA <- bpmapToProbeAnno(bpmap,uniqueSeq=F) > IP_ratio <- getRatio(loess_expt, ip=IP, control=INP, description="K4me3 expt vs control") > peaks <- cmarrt.ma(IP_ratio, pA, chr=chrs, M=NULL, frag.length=300) > plotcmarrt(peaks) output looks just fine. But this call fails and I have scoured the 'net looking for an answer: > peaklist <- cmarrt.peak(peaks,alpha=0.05,method="BH",minrun=4,asCherList=T) [1] "Zero bound probe found under correlation structure" Creating cherList Error in validObject(.Object) : invalid class ?cher? object: FALSE In addition: Warning message: In validityMethod(object) : Slots 'name','chromosome','start','end','antibody','maxLevel',and 'score' may each only contain one element. > sessionInfo() R version 2.15.3 (2013-03-01) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] biomaRt_2.14.0 Starr_1.14.1 affxparser_1.30.2 affy_1.36.1 [5] Ringo_1.22.0 Matrix_1.0-11 lattice_0.20-14 limma_3.14.4 [9] RColorBrewer_1.0-5 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 annotate_1.36.0 AnnotationDbi_1.20.7 [4] BiocInstaller_1.8.3 DBI_0.2-5 genefilter_1.40.0 [7] IRanges_1.16.6 MASS_7.3-23 parallel_2.15.3 [10] preprocessCore_1.20.0 pspline_1.0-15 RCurl_1.95-4.1 [13] RSQLite_0.11.2 splines_2.15.3 stats4_2.15.3 [16] survival_2.37-4 tools_2.15.3 vsn_3.26.0 [19] XML_3.96-0.1 xtable_1.7-1 zlibbioc_1.4.0