[BioC] Error using Ringos readNimblegen

Morten Hansen mhansen at imbg.ku.dk
Wed May 28 11:17:59 CEST 2008

I have a problem with the Ringo package.

I am trying to read in the results from a 1.5Kb Human Promoter Array 
(CHP0150-HP1). I get the following error shown in below in the "Output" 

The target.txt, spottype.txt and sessionInfo() is shown below the 
"Output" section.

*** Output ***
 > myDir <- c("/home/mhansen/R/ChIP-chip/39037")
 > myRg <- readNimblegen("targets.txt","spottypes.txt", path = myDir)
Reading targets file...
Reading raw intensities...
Read header information
Read /home/mhansen/R/ChIP-chip/39037/39037_532_pair.txt
Read /home/mhansen/R/ChIP-chip/39037/39037_635_pair.txt
Error in RG$R[, i] <- obj[, columns$f] :
   number of items to replace is not a multiple of replacement length

The target.txt and spottype.txt look like this:
*** target.txt ***
SlideNumber     FileNameCy3     FileNameCy5     Species Cy3     Cy5
HSAP0406        39037_532_pair.txt      39037_635_pair.txt      Homo 
sapiens (human)    total   HSAP0406

*** spottype.txt ***
SpotType        GENE_EXPR_OPTION        PROBE_ID        Color
Probe   BLOCK1  *       black

*** sessionInfo()***
 > sessionInfo()
R version 2.6.2 (2008-02-08)


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

other attached packages:
  [1] Ringo_1.2.0          RColorBrewer_1.0-2   vsn_3.2.1 
affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1         limma_2.12.0
  [8] geneplotter_1.16.0   lattice_0.17-8       annotate_1.16.1 
xtable_1.5-2         AnnotationDbi_1.0.6  RSQLite_0.6-8
DBI_0.2-4         [15] Biobase_1.16.3

loaded via a namespace (and not attached):
[1] grid_2.6.2         KernSmooth_2.22-22 rcompgen_0.1-17

Any suggestions?

Morten Hansen MD
ICMM, Panum institute
University of Copenhagen
Email: mhansen at imbg.ku.dk

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