Hi,

I have problem in reading my .xys files using the function read.xysfiles 
in Oligo package (I have created my .xys based on my .pair files 
following instruction I found on [BioC]).

Here is what I have done:

>basename(xys)
  [1] "Drained_control_1.xys"         "Drained_control_2.xys"         "Drained_control_3.xys"
  [4] "Drained_infected_resist_1.xys" "Drained_infected_resist_2.xys" "Drained_infected_resist_3.xys"
  [7] "Drained_infected_suscep_1.xys" "Drained_infected_suscep_2.xys" "Drained_infected_suscep_3.xys"
[10] "Drained_wounding_1.xys"        "Drained_wounding_2.xys"        "Drained_wounding_3.xys"
>is.character(xys)
[1] TRUE
>read.xysfiles(xys, pd.110224.pinus.fa.exp.modified)
Error: is.character(filenames) is not TRUE

>sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252

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

other attached packages:
  [1] pd.110224.pinus.fa.exp.modified_0.0.1 pdInfoBuilder_1.26.0                  oligo_1.26.2
  [4] Biostrings_2.30.1                     XVector_0.2.0                         IRanges_1.20.6
  [7] oligoClasses_1.24.0                   affxparser_1.34.2                     RSQLite_0.11.4
[10] DBI_0.2-7                             Biobase_2.22.0                        BiocGenerics_0.8.0

loaded via a namespace (and not attached):
  [1] affyio_1.30.0         BiocInstaller_1.12.0  bit_1.1-11            codetools_0.2-8       ff_2.2-12
  [6] foreach_1.4.1         GenomicRanges_1.14.4  iterators_1.0.6       preprocessCore_1.24.0 splines_3.0.2
[11] stats4_3.0.2          tools_3.0.2           zlibbioc_1.8.0



(I have previously created the annotation package 
"pd.110224.pinus.fa.exp.modified"with pdInfoBuilder using 
"Drained_control_1.xys" as template with apparently no problems and I 
have installed it).

Sorry if this is a stupid problem, I´m learning R and Bioconductor at 
the same time in these weeks but I couldn´t find info about this problem.

Thanks for your help!

Tommaso

-- 
Tommaso Raffaello, PhD

University of Helsinki
Department of Forest Sciences
Latokartanonkaari 7 PO Box 27
00014 Helsinki (Finland)

Phone number: +358 504486086
email: tommaso.raffaello@helsinki.fi
email: tommaso.raffaello@gmail.com


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