[BioC] bead-level data from Infinium methylation arrays

Mark Dunning mark.dunning at gmail.com
Wed Jul 8 11:16:54 CEST 2009

Hi Tim,

Do you know what scanning software was used to create these bead-level
data? BeadScan or the newer iScan system? I'm wondering if the format
of the files has changed since we wrote readIllumina. When the object
'dat1' is created in readIllumina it assumes a set number of columns
in the bead-level text files (4,6 or 7) so if the number of columns is
something different then this dat1 object will not be created causing
the function to error.

Are you able to read in the .txt files and print out the first 10
lines so that I can see what columns there are in the file?



On Tue, Jul 7, 2009 at 11:46 PM, Tim Triche, Jr.<ttriche at usc.edu> wrote:
> Hello bioconductor-list subscribers,
>   I am interested in various approaches to preprocessing and normalizing
> Infinium data, some rather different from Illumina's.  I noticed that the
> 'beadarray' package has the ability to read in bead-level data, and while
> I'm sure this isn't the most scalable solution, given the way that Infinium
> arrays are structured, the thought occurred that dealing with one problem at
> a time (eg. reading the data into a sensible structure, THEN dealing with
> memory issues perhaps using R.huge etc.) might be a good idea.
>  From the raw data, I constructed a 'targets' file (attached) and then
> attempted to pull in the bead-level information from a couple of arrays (so
> as not to exceed my laptop's RAM; I have raw data for 72 arrays on 8 slides
> to start with):
>> Mack <- readIllumina(arrayNames = targets$ArrayName,
>                       targets=targets, backgroundMethod = "none",
>                       singleChannel=FALSE, metrics=TRUE)
> Found 2 arrays
> Error in order(dat1$ProbeID) : object 'dat1' not found
> In addition: Warning message:
> In readIllumina(arrayNames = targets$ArrayName, targets = targets,  :
>  No annotation package was specified.
>  Need to use SetAnnotation later
> The data structure 'dat1' is buried within a switch statement and each
> branch can apparently throw the error message seen above.  I assume that,
> once I get the data read into a reasonable form, I can deal with the lack of
> annotation files later (in fact, I ought to be able to extract that from
> Illumina's own manifest, correct?).  But the current error is puzzling me
> and there is no point (for my project) working with anything other than
> bead-level data.  On the off chance that someone else has seen this before,
> I figured I'd try the list.
> Any assistance, suggestions, constructive criticism ("hey why aren't you
> using 'otherpackage'!?!"), etc. would be most appreciated.
> Thanks in advance,
> --tim
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