[BioC] cmarrt.peak function does not work

[Susan Wilson]

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