Entering edit mode
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