Search
Question: Ringo Plots Only Partially Made
0
gravatar for bruce.moran
2.4 years ago by
bruce.moran20
Ireland
bruce.moran20 wrote:

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

 

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by bruce.moran20
0
gravatar for bruce.moran
2.4 years ago by
bruce.moran20
Ireland
bruce.moran20 wrote:

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.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by bruce.moran20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 118 users visited in the last hour