Matt Ritchie wrote:
> Hi Ina,
> What operating system are you using? If you are on Windows, I have
> version of beadarray under R-2.5.1 and made it available at our
> anonymous ftp server:
> login: anonymous
> password: your email address
> Best wishes,
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"),
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
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
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
>>> I noticed a problem reading in BeadStudio 3 output a few weeks ago
>>> checked in a fix to the developmental version of beadarray.
>>> So if you upgrade to the latest version of beadarray (1.5.8,
>> Matt, this version was built under R 2.6, but the latest R version
>> I have (and that I can find) is R.2.5.1 - after installing this
>> I am getting error messages after I load the package with
>> Error in loadNamespace(name) : there is no package called
>> 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
>> (I don't find the package 'AnnotationDbi' in the list of
>> Any suggestion?
>> Many thanks, Ina
>>> your summary
>>> data should read in without incident. Note that the default
>>> 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(),
>>> will help diagnose the cause of the second error you mention (most
>>> you are missing the tiff files, so try useImages=FALSE).
>>> Best wishes,
>>>> I am still struggling with my first try at working with
>>>> array expression data, specifically getting the data read by the
>>>> 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)
>>>> 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
>>>> I read the summary data(2) with the statement
>>>> readBeadSummaryData(dataFile, skip=8, columns = list(exprs =
>>>> "AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS"),
>>>> 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
>>>> 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.