Hi Huber,

The following is the output of sessionInfo().
R version 2.6.1 (2007-11-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
 [1] arrayQualityMetrics_1.2.1 latticeExtra_0.3-1
CCl4_1.0.7                simpleaffy_2.14.05
 [5] affyPLM_1.14.0            gcrma_2.10.0
matchprobes_1.10.0        RColorBrewer_1.0-2
 [9] vsn_3.2.1                 limma_2.12.0
affy_1.16.0               preprocessCore_1.0.0
[13] affyio_1.6.1              genefilter_1.16.0
survival_2.34             geneplotter_1.16.0
[17] lattice_0.17-2            annotate_1.16.1
xtable_1.5-2              AnnotationDbi_1.0.6
[21] RSQLite_0.6-8             DBI_0.2-4
Biobase_1.16.3

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-21

The array1is a NChannelSet created from the RGList using the following
command.
array1<-new("NChannelSet")

Regards,
Abhilash

On Fri, Apr 18, 2008 at 8:04 PM, Wolfgang Huber <huber@ebi.ac.uk> wrote:

> Dear Abhilash
>
> > As you directed, I tried arrayQualityMetrics. I used feature extracted
> txt
> > file  from Agilent  arrays and created RGList. It has given the
> following
> > error, I am wondering whether it is  because I didnot try to create
> > assayData, featureData and phenoData.
> > arrayQualityMetrics(expressionset = array1,
> > + outdir = "array")
> > *The directory 'array' has been created.
> > Error in seq_len(ncol(x)) : argument must be non-negative
> >
> > *What could I do to solve this problem?
>
> First of all, give the output of sessionInfo().
> Second, you could tell us a bit more about what "array1" is.
>
>  Best wishes
>         Wolfgang
>
> > Regards,
> > Abhilash
> >
> >
> > On Wed, Apr 16, 2008 at 11:07 PM, Wolfgang Huber <huber@ebi.ac.uk>
> wrote:
> >
> >> Dear Abilash,
> >>
> >> you could try to run the arrayQualityMetrics report from the eponymous
> >> package (and preferably a current devel version [1]). The plots in
> there
> >> would help you to assess both whether there are gross problems in the
> >> data, and how much and what type of normalisation is needed.
> >>
> >> Adequate normalisation removes unwanted technical variation while it
> >> maintains the interesting biological signal in the data. The best way
> to
> >> assess whether this is goal is achieved is by looking at the behaviour
> >> of the controls that were done as part of the experiment.
> >>
> >> [1]
> >>
> >>
> http://www.bioconductor.org/packages/2.2/bioc/html/arrayQualityMetrics.html
> >>
> >> Best wishes
> >>  Wolfgang
> >>
> >> ------------------------------------------------------------------
> >> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> >>
> >>
> >> 16/04/2008 18:02 Abhilash Venu a écrit
> >>> Hi all,
> >>>
> >>> I have a few questions. I am analyzing  20 experiments  performed  in
> >>> Agilent 4x44K. Tumor and adjacent normal were labeled with Cy5 and Cy3
> >>> respectively. The experiments include two dye swaps also. The feature
> >>> extraction were performed using Agilent feature extraction software
> >> version
> >>> 8.5. The txt files obtained after feature extraction, subjected to
> >> further
> >>> analysis by limma. The script has given below
> >>> txt_files <- dir(pattern=".txt")
> >>> RG<-read.maimages(txt_files, source="agilent")
> >>> design<-c(1,1,1,1,1,1,1,1,1,1,1,-1,1,1,1,1,1,1,1,-1) # this include
> two
> >> dye
> >>> swap also
> >>> Rgene<-backgroundCorrect(RG,method="normexp")
> >>> fit<-lmFit(Rgene,design)
> >>> fit<-eBayes(fit)
> >>> topTable(fit,adjust="fdr", number=100)
> >>>
> >>> As a result I get the format in which 'B' indicates what parameter?
> And
> >> is
> >>> this analysis method is enough to get a good data?
> >>> In Agilent arrays, I think generally it is normalized, in that case
> how
> >> the
> >>> data will be affected by normalizing it again using above method?
> >>> How can we decide which normalization methods should be used? Do you
> >> think
> >>> its always better to decide by plotting different graphs?
> >>>
> >>> Comments and answers will be appreciated.
> >>>
> >>> Regards,
> >>> Abhilash
> >>>
> >>>
> >
> >
> >
>



-- 

Regards,
Abhilash

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