[BioC] Illumina bead arrays

[Ina Hoeschele]

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
>>>>     
>>>>