Question: cmarrt.peak function does not work
gravatar for Susan Wilson
4.7 years ago by
Susan Wilson50
Susan Wilson50 wrote:
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 <-, 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
ADD COMMENTlink written 4.7 years ago by Susan Wilson50
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 105 users visited in the last hour