Hi Dear list,

i am a newbie who just start the learning of BioC
i installed the getMonograph and follow the steps of the book
"Bioinformatics and Computational Biology Solutions Using R and
Bioconductor"

i encountered a problem when do the following step by step exercise:

and can someone tell me a little better way to study how to use BioConductor
to analysis microarray data?
Thanks!


 R

R version 2.5.0 (2007-04-23)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
> library("SpikeInSubset")
> data(spikein95)
> pd <- data.frame(population = c(1,1,1,2,2,2),replicate = c(1,2,3,1,2,3))
> rownames(pd) <- sampleNames(spikein95)
> vl <- list(population = "1 is control, 2 is treatment", replicate =
c(arbitraty numbering))
Error: syntax error, unexpected SYMBOL, expecting ',' in "vl <-
list(population = "1 is control, 2 is treatment", replicate = c(arbitraty
numbering"
> vl <- list(population = "1 is control, 2 is treatment", replicate =
"arbitraty numbering")
> phenoData(spikenin95) <- new("phenoData", pData = pd, varLabels = vl)
Error in phenoData(spikenin95) <- new("phenoData", pData = pd, varLabels =
vl) :
        object "spikenin95" not found
In addition: Warning message:
The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
> AnnotatedDataFrame(spikenin95) <- new("AnnotatedDataFrame", pData = pd,
varLabels = vl)
Error in .nextMethod(.Object, ...) : invalid names for slots of class
"AnnotatedDataFrame": pData, varLabels
> AnnotatedDataFrame(spikenin95) <- new("phenoData", pData = pd, varLabels =
vl)
Error in AnnotatedDataFrame(spikenin95) <- new("phenoData", pData = pd,  :
        object "spikenin95" not found
In addition: Warning message:
The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
> AnnotatedDataFrame(spikenin95) <- new("ExpressionSet", pData = pd,
varLabels = vl)
Error in function (storage.mode = c("lockedEnvironment", "environment",  :
        'AssayData' elements with invalid dimensions: 'varLabels'
> ls ()
[1] "pd"        "spikein95" "vl"

> sessionInfo()
R version 2.5.0 (2007-04-23)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;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=C

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

other attached packages:
SpikeInSubset          affy        affyio       Biobase
      "1.2.4"      "1.14.0"       "1.4.0"      "1.14.0"
> capabilities()
    jpeg      png    tcltk      X11 http/ftp  sockets   libxml     fifo
    TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE
  cledit    iconv      NLS  profmem
    TRUE     TRUE     TRUE    FALSE
-- 
Daofeng.Li

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