[BioC] Issue with Genome Graphs

[Jeremy Ng]

Dear List,

I have been trying to use GenomeGraphs for the mapping of exon array information. Specifically, I am using it to generate a diagram reflecting the exon normalised score (defined as log2 (probes) - log2 (transcript cluster) ).

These scores are generated in Excel, and thereafter imported as a text file into my R workspace. 

I realised that I have an issue with plotting. I keep getting this error message whenever I do gdPlot

Warning messages:
1: In min(obj at ens[, "exon_chrom_start"]) :
  no non-missing arguments to min; returning Inf
2: In max(obj at ens[, "exon_chrom_end"]) :
  no non-missing arguments to max; returning -Inf

Can anyone enlighten me on what I have done wrong to return this error message? I used the codes as below:

mart<-useMart("ensembl", dataset="hsapiens_gene_ensembl")
ctl4.gene<-makeGene("hgnc_symbol", id="ctl4", biomart= mart)
gdPlot(ctl4.gene)

This same error message appears even when I try to plot for transcript.

On a side note, I know that I can do RMA normalisation for the Affy HuEx 1.0 platform at the exon level (probeset level) using packages such as oligo or simpleaffy, or fRMA using the package fRMA. However, I was wondering if I can actually do RMA normalisation at the transcript (gene) level using any packages? And perhaps, even do the generation of the normalised scores on R itself as well? At present I use APT to do both RMA normalisations at the gene and exon level, then manipulate in Excel before I import all the data into R for plotting.

There is also this other error message which appeared:

Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] : 
  non-numeric argument to binary operator

At this point, I know that this error arose when I was making the exons using the makeExonArray function in gdPlot. However, I am not clear as to which particular argument was the cause of this error message. Will anyone be able to advise on which particular argument was the cause of this? MakeExonArray codes are as follows:

ctl4.exons <- makeExonArray(intensity = ctl4.inclusion.matrix, probeStart = ctl4.probes$start, probeEnd = ctl4.probes$stop, probeId = as.character(ctl4.probes$probeset_id), nProbes = ctl4.probes$probe_count, dp = DisplayPars(color = ctl4.cols))

Where, ctl4.inclusion.matrix is a matrix using as.matrix from a .txt file containing the normalised scores, ctl4.probes is a list of probes for the gene (CTL4) and the annotations as appended in the Affymetrix exon annotation file (the CSV).
  
SessionInfo as bellows:
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GenomeGraphs_1.18.0 biomaRt_2.14.0     

loaded via a namespace (and not attached):
[1] RCurl_1.95-3 tools_2.15.2 XML_3.95-0.1

Thank you so much for any help offered and sorry for the long post! 

Best,
Jeremy
National University of Singapore