[BioC] About beadarray package

[ssls sddd]

Hi Alice,

I used:

library(beadarray)
dataFile = "RawData_bkg_092107_Beadarrays.csv"
BSData <- readBeadSummaryData(dataFile, ProbeID="TargetID",skip=0,columns =
list(exprs = "AVG_Signal", BeadStDev = "BEAD_STDEV",NoBeads = "Avg_NBEADS"))

I have attached a snapshot of first few lines of data.

Thanks for the help!

Alex

On 10/1/07, Johnstone, Alice <Alice.Johnstone at esr.cri.nz> wrote:
>
> What is the command you are using, and what do the first few lines of
> your data file look like?
>
>
> ________________________________
>
>         From: ssls sddd [mailto:ssls.sddd at gmail.com]
>         Sent: Tuesday, 2 October 2007 4:01 p.m.
>         To: Johnstone, Alice
>         Cc: bioconductor at stat.math.ethz.ch
>         Subject: Re: [BioC] About beadarray package
>
>
>         The result of sessionInfo () reads as below. But I think it is
> up-to-date.
>
>         Thanks!
>
>         Alex
>
>         > sessionInfo()
>         R version 2.5.1 (2007-06-27)
>         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"      "tools"     "stats"     "graphics"  "grDevices"
> "utils"
>         [7] "datasets"  "methods"   "base"
>
>         other attached packages:
>            beadarray beadarraySNP  quantsmooth      lodplot     quantreg
> SparseM
>              "1.4.0"      " 1.2.0"      "1.2.0"        "1.1"
> "4.10"       "0.73"
>                 affy       affyio  geneplotter      lattice     annotate
> Biobase
>             "1.14.2"      " 1.4.1"     "1.14.0"    "0.15-11"
> "1.14.1"     "1.14.1"
>                limma
>             "2.10.5"
>
>
>
>         On 10/1/07, Johnstone, Alice <Alice.Johnstone at esr.cri.nz> wrote:
>
>
>                 What version of beadarray are you using?  You might need
> to update it to
>                 the latest version.
>                 To ensure you get prompt help your post needs to include
> the output of:
>
>                 sessionInfo()
>
>
>                 Cheers
>                 Alice
>
>                 > -----Original Message-----
>                 > From: bioconductor-bounces at stat.math.ethz.ch
>                 > [mailto: bioconductor-bounces at stat.math.ethz.ch
> <mailto:bioconductor-bounces at stat.math.ethz.ch> ] On Behalf Of ssls sddd
>                 > Sent: Tuesday, 2 October 2007 2:43 p.m.
>                 > To: bioconductor at stat.math.ethz.ch
>                 > Subject: [BioC] About beadarray package
>                 >
>                 > Hello! I tried to read in data using the function
>                 > readBeadSummaryData() but I got the error message
> like:
>                 >
>                 > Error in `rownames<-`(`*tmp*`, value = c(41306L,
> 35002L,
>                 > 16863L, 12131L,  :
>                 >         attempt to set rownames on object with no
> dimensions
>                 >
>                 >
>                 > I tried the sample data called 'raw_data.csv' and got
> quite
>                 > similar error
>                 > message:
>                 >
>                 > Error in `rownames<-`(`*tmp*`, value = c(1L, 2L, 3L,
> 4L, 5L,
>                 > 6L, 7L, 8L,  :
>                 >         attempt to set rownames on object with no
> dimensions
>                 >
>                 >
>                 > can anyone suggest how to correct this?
>                 >
>                 > Thank you very much!
>                 >
>                 > Alex
>                 >
>                 >       [[alternative HTML version deleted]]
>                 >
>                 > _______________________________________________
>                 > Bioconductor mailing list
>                 > Bioconductor at stat.math.ethz.ch
> <mailto:Bioconductor at stat.math.ethz.ch>
>                 > https://stat.ethz.ch/mailman/listinfo/bioconductor
>                 > Search the archives:
>                 >
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>                 >
>
>
>
>
>
>
> P Think before you print
> This e-mail transmission and any attachments that accompany it may contain
> information that is privileged, confidential or otherwise exempt from
> disclosure under applicable law and is intended solely for the use of the
> individual(s) to whom it was intended to be addressed.
> If you have received this e-mail by mistake, or you are not the intended
> recipient, any disclosure, dissemination, distribution, copying or other use
> or retention of this communication or its substance is prohibited. If you
> have received this communication in error, please immediately reply to the
> author via e-mail that you received this message by mistake and also
> permanently delete the original and all copies of this e-mail and any
> attachments from your computer. Thank you.
>
>