Hi,

I have been following the standard guides for Starr and Ringo for analysis of my Affy tiling array data. It works well, and I get enriched regions and so forth. I would like to make plots from 'cher' (code chunk number 25: plotCher form Ringo link).

I run:

plot(chers[[1]], expst_ratio_smooth, probeAnno=probeAnno, gff=transcriptAnno, paletteName="Spectral")

Error in if (x == -1) return("-") : missing value where TRUE/FALSE needed

Traceback of which is:

8: FUN(X[[i]], ...)
7: lapply(X = X, FUN = FUN, ...)
6: sapply(gff$strand, translateStrand)
5: plotFeatures(gff = gff, chr = chrom, xlim = xlim, strand = strand,
       featureExclude = featureExclude, featureColorScheme = 1,
       vpr = which(names(VP) == sprintf("gff%s", strand)), ...)
4: chipAlongChrom(y, chrom = x@chromosome, samples = samples, xlim = c(x@start -
       extent, x@end + extent), probeAnno = probeAnno, gff = gff,
       ...)
3: .local(x, y, ...)
2: plot(chers[[1]], expst_ratio_smooth, probeAnno = probeAnno, gff = transcriptAnno,
       paletteName = "Spectral")
1: plot(chers[[1]], expst_ratio_smooth, probeAnno = probeAnno, gff = transcriptAnno,
       paletteName = "Spectral")

The plots are partially made, with y-axis and points/lines for some data but not others. No x-axis (chromosome, position) is plotted. I use annotation from an Ensembl GFF that does not have feature names (all are 'regulatory region' for types), but I presume this is not an issue. Otherwise analysis uses 'stock' input (CEL, bpmap).

Help much appreciated,

Thanks,

Bruce.

R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_IE.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_IE.UTF-8        LC_COLLATE=en_IE.UTF-8
 [5] LC_MONETARY=en_IE.UTF-8    LC_MESSAGES=en_IE.UTF-8
 [7] LC_PAPER=en_IE.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] Starr_1.24.0        affxparser_1.40.0   affy_1.46.1
 [4] Ringo_1.32.0        lattice_0.20-31     Matrix_1.2-2
 [7] limma_3.24.13       RColorBrewer_1.1-2  Biobase_2.28.0
[10] BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.30.1  MASS_7.3-42           splines_3.2.0
 [4] zlibbioc_1.14.0       IRanges_2.2.5         pspline_1.0-17
 [7] xtable_1.7-4          GenomeInfoDb_1.4.1    tools_3.2.0
[10] DBI_0.3.1             genefilter_1.50.0     survival_2.38-3
[13] preprocessCore_1.30.0 affyio_1.36.0         S4Vectors_0.6.1
[16] RSQLite_1.0.0         BiocInstaller_1.18.3  stats4_3.2.0
[19] XML_3.98-1.3          annotate_1.46.1       vsn_3.36.0

Sorry, just caught the issue, transcriptAnno had no strand info so changing all to "+" removes the error.

Apologies.

Also this is why to use traceback() =D

Bruce.