[BioC] Illumina bead arrays

[Ina Hoeschele]

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
>>