 Madison, 20 may 2009Hello all, I was wondering if anyone would have an idea about the error I describe below:SessionInfo() at the very end of the mail.Data: Nimblegen arrays for methylation. Chips are new high density chips.Method: use functions in the Ringo package to read-in the data that is then supposed to become an RGList based on the limma package:The read-in method is a bit convoluted but I followed the example in the Ringo package and in the supplement to the paper "Analuzing ChIP-chip data using Bioconductor" - Toedling and Huber - PLOS Nov 2008 vol 4 Issue 11:First the spottypes.txt file describing spots:$ cat spottypes.txt 
SpotType        GENE_EXPR_OPTION        PROBE_ID        Color
Probe   BLOCK1  *       blackThen the text files containing the names of the 2-color data- there are 3 files but here is the first one:$ cat files_hyb1.txt 
SlideNumber     FileNameCy3     FileNameCy5     Species Cy3     Cy5
HYB12um Hyb1_532.pair   Hyb1_635.pair   Homo sapiens (human)    C3      C5Then read-in the data according to the paper:> library(Ringo)
> sprintf("files_hyb%d.txt",1:3)
[1] "files_hyb1.txt" "files_hyb2.txt" "files_hyb3.txt"
> RGs <- lapply(sprintf("files_hyb%d.txt",1:3),readNimblegen, "spottypes.txt", path=".")
Reading targets file...
Reading raw intensities...
Read header information
Read ./Hyb1_532.pair 
Read ./Hyb1_635.pair 
Determining probe categories...
Matching patterns for: GENE_EXPR_OPTION PROBE_ID 
Found 2170021 Probe 
Setting attributes: values Color 
[...etc...]
> head(RGs[[1]]$R)
     Hyb1_635
[1,]  3062.94
[2,]  3881.24
[3,]  3863.27
[4,] 14933.02
[5,]  6925.96
[6,]  8083.06
>> print(RGs)
[[1]]
An object of class "RGList"
$R
[1]  3062.94  3881.24  3863.27 14933.02  6925.96
2173621 more rows ...$G
[1]  3316.29  4459.45  4492.16 15431.71  7694.10
2173621 more rows ...$Rb
[1] 0 0 0 0 0
2173621 more rows ...$Gb
[1] 0 0 0 0 0
2173621 more rows ...$genes
  GENE_EXPR_OPTION            PROBE_ID POSITION    X    Y Status
1           BLOCK1 BD_10X23FS000000445      445  689 1253  Probe> class(RGs)
[1] "list"
> So it does say that is is an object of class RGList....Reading further in the Ringo vignette I found the following:Among the provided alternative preprocessing options is also the Tukey-biweight scaling procedure that NimbleGen have used to scale ChIP-chip readouts so that the data is centered  on zero.
> exampleX.NG <- preprocess(exRG, method="nimblegen")
> sampleNames(exampleX.NG) <- sampleNames(exampleX)So I tried to apply that to the RG list I just created but have an "inherit" error:> RGs.NG <- preprocess(RGs, method ="nimblegen")
Error: inherits(myRG, "RGList") is not TRUEI therefore tried other variation, including a suggestion on the BioConductor listserv but the error persists:> xyz <- preprocess(RGs, method="loess", returnMAList=TRUE)
Error: inherits(myRG, "RGList") is not TRUE

> xyz <- preprocess(RGs[RGs$genes$Status=="Probe",], method="loess", returnMAList=TRUE)
Error in RGs[RGs$genes$Status == "Probe", ] : 
  incorrect number of dimensionsQuestion: where does this "inherit" problem comes from ?The Nimblegen data files (.pair files) are longer because it is a high density array but that should not change the type of the data structure I would think.Thank you for any suggestions,Jean-Yves Sgro - jsgro@wisc.edu------------------------------------------------
Jean-Yves Sgro, Ph.D., Senior Scientist
http://myprofile.cos.com/sgroj65
------------------------------------------------
University of Wisconsin 
Biotechnology Center Gene Expression Center
425 Henry Mall Madison Wi 53706 USA
http://www.biotech.wisc.edu/ServicesResearch/Gec/
Fax: 608-262-6748
------------------------------------------------
& Institute for Molecular Virology
1525 Linden Drive Madison WI 53706
tel: 608-262-7464
http://virology.wisc.edu/virusworld
------------------------------------------------> sessionInfo()
R version 2.9.0 (2009-04-17) 
x86_64-redhat-linux-gnulocale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=Cattached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     other attached packages:
[1] Ringo_1.8.0        Matrix_0.999375-24 lattice_0.17-22    limma_2.18.0      
[5] RColorBrewer_1.0-2 Biobase_2.4.1     loaded via a namespace (and not attached):
[1] annotate_1.22.0     AnnotationDbi_1.6.0 DBI_0.2-4          
[4] genefilter_1.24.0   grid_2.9.0          RSQLite_0.6-8      
[7] splines_2.9.0       survival_2.35-4     xtable_1.5-5       
> 

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