Hi Ina,
What does line 343 look like?  The line number reported discounts the
skipped lines so when you open the file to look at it you have to take this
into account.
Mike Smith


On 8/23/07, Ina Hoeschele <inah@vt.edu> wrote:
> >
> > Matt Ritchie wrote:
> > > Hi Ina,
> > >
> > > What operating system are you using?  If you are on Windows, I have
> > built a
> > > version of beadarray under R-2.5.1 and made it available at our
> > institute's
> > > anonymous ftp server:
> > >
> > > ftp://ftp.cancerresearchuk.org/pub/any/beadarray/beadarray_1.5.8.zip
> > > login: anonymous
> > > password: your email address
> > >
> > > Best wishes,
> > >
> > > Matt
> > >
> > >
> > Matt,
> >     I downloaded this version but I am still getting an error message
> > while reading the data, please see below.
> > > readBeadSummaryData(dataFile, skip=7, columns = list(exprs =
> > + "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"),
> > sep="\t")
> > Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
> > na.strings,  :
> >         line 336 did not have 98 elements
> > (when I look at line 336 it does not look any different from the other
> > lines, this is the same error that I had before, I also changed skip to
> > 8 but this does not help, it then complains about line 335).
> > Many thanks, Ina
> >
> > >> Matt Ritchie wrote:
> > >>
> > >>> Hi Ina,
> > >>>
> > >>> Sorry to hear you are having such a struggle reading in your
> > Illumina data.
> > >>> I noticed a problem reading in BeadStudio 3 output a few weeks ago
> > and
> > >>> checked in a fix to the developmental version of beadarray.
> > >>>
> > >>> So if you upgrade to the latest version of beadarray (1.5.8,
> > available from
> > >>> http://bioconductor.org/packages/2.1/bioc/html/beadarray.html)
> > >>>
> > >> Matt, this version was built under R 2.6, but the latest R version
> > that
> > >> I have (and that I can find) is R.2.5.1 - after installing this
> > package
> > >> I am getting error messages after I load the package with
> > >> library(beadarray):
> > >> Error in loadNamespace(name) : there is no package called
> > 'AnnotationDbi'
> > >> In addition: Warning message: package 'beadarray' was built under R
> > >> version 2.6.0
> > >> Error in as.environment(pos) : no item called "newtable" on the
> > search list
> > >>
> > >> (I don't find the package 'AnnotationDbi' in the list of downloadable
> >
> > >> packages).
> > >>
> > >> Any suggestion?
> > >> Many thanks, Ina
> > >>
> > >>> your summary
> > >>> data should read in without incident.  Note that the default
> > arguments to
> > >>> readBeadSummaryData() have been set for BeadStudio 3 output, so all
> > you need
> > >>> to set it the filename.
> > >>>
> > >>> I have also added some more meaningful warnings to readIllumina(),
> > which
> > >>> will help diagnose the cause of the second error you mention (most
> > likely
> > >>> you are missing the tiff files, so try useImages=FALSE).
> > >>>
> > >>> Best wishes,
> > >>>
> > >>> Matt
> > >>>
> > >>>
> > >>>
> > >>>> Hi,
> > >>>>    I am still struggling with my first try at working with Illumina
> > bead
> > >>>> array expression data, specifically getting the data read by the R
> > >>>> package beadarray.
> > >>>>
> > >>>> The data was created by an off-site collaborator using BeadStudio
> > >>>> version  3.0.14. My collaborator sent two types of files to me:
> > >>>> (1) a number of .csv files (read by excel, 2 for each sample) with
> > >>>> columns Illumicode, N, mean GRN, Dev GRN.
> > >>>> (2) a summary .txt file with columns TargetID
> > >>>> MIN_Signal-1814647013_A    AVG_Signal-1814647013_A
> > >>>> MAX_Signal-1814647013_A    NARRAYS-1814647013_A
> > >>>> ARRAY_STDEV-1814647013_A    BEAD_STDEV-1814647013_A
> > >>>> Avg_NBEADS-1814647013_A    Detection-1814647013_A, with the
> > >>>> MIN_Signal-... to Detection-... columns repeated for the remaining
> > samples.
> > >>>>
> > >>>> I read the summary data(2) with the statement
> > >>>> readBeadSummaryData(dataFile, skip=8, columns = list(exprs =
> > >>>> "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"),
> > sep="\t"),
> > >>>> but every time I do this R gets hung up (no error message).
> > >>>>
> > >>>> I also tried reading the bead-level data (the .csv files) with the
> > statement
> > >>>> BLData <- readIllumina(textType = ".csv")
> > >>>> but then I get the error message
> > >>>> Error in strtrim(x, width) : invalid 'width' argument
> > >>>>
> > >>>> Any suggestions would be much appreciated.
> > >>>> Thank you.
> > >>>> Ina
> > >>>>
> > >>>>
> >
> > _______________________________________________
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> >
>
>

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