Dear Kristof De Beuf and Bioconductors,

I tried to use  waveTiling package to analysis AGRONOMICS1 tiling
array data. An error message happened when I run bgCorrQn function,
even I used data from build-in data package.

Could you please help me to get the bgCorrQn function work? or any
other suggestion for working with  AGRONOMICS1 tiling arrays?


Thank you very much


Yanwu Guo


> leafdev <- as(leafdev,"WaveTilingFeatureSet")> leafdevBQ <- bgCorrQn(leafdev,useMapFilter=leafdevMapAndFilterTAIR9)Error in exprs(object[pmIndex, ]) :
  error in evaluating the argument 'object' in selecting a method for
function 'exprs': Error in validObject(.Object) :
  invalid class "WaveTilingFeatureSet" object: featureNames differ
between assayData and featureData> sessionInfo()R version 3.0.2
(2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] waveTilingData_0.99.3
BSgenome.Athaliana.TAIR.TAIR9_1.3.18 BSgenome_1.30.0
 [4] GenomicRanges_1.14.4                 pd.atdschip.tiling_0.0.6
        RSQLite_0.11.4
 [7] DBI_0.2-7                            BiocInstaller_1.12.0
        waveTiling_1.4.0
[10] GenomeGraphs_1.22.0                  biomaRt_2.18.0
        oligo_1.26.1
[13] Biostrings_2.30.1                    XVector_0.2.0
        IRanges_1.20.6
[16] Biobase_2.22.0                       oligoClasses_1.24.0
        BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] affxparser_1.34.0     affy_1.40.0           affyio_1.30.0
bit_1.1-11            codetools_0.2-8
 [6] ff_2.2-12             foreach_1.4.1         iterators_1.0.6
preprocessCore_1.24.0 RCurl_1.95-4.1
[11] splines_3.0.2         stats4_3.0.2          tools_3.0.2
waveslim_1.7.3        XML_3.98-1.1
[16] zlibbioc_1.8.0

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