[BioC] R command readIllumina with beadarray

Matthew Ritchie mritchie at wehi.EDU.AU
Mon Oct 4 01:29:17 CEST 2010

Dear Hajar,

If this is the same data you mailed the list about the other day, make
sure the 'arrayNames' you are specifying are the full names (probably
something like '5513091009_A_1_perBeadFile.txt',
'5513091009_A_2_perBeadFile.txt' for your first sample if you have WG-6
BeadChips, etc.)

Also make sure that all of these files are available in the current
working directory - you can check this with


If they aren't, change the working directory using the setwd() function.

Best wishes,


> Hi everyone,
> I practiced using "Analysing Illumina bead-based data using beadarray by
> Richie & Dunning with the SAMExample dataset. However, when exploring my
> own beadarraydata I found that my raw data files are txt files and not csv
> (as they were in the practical).
> I was able to read the metrics.txt file (this file gives me the date of
> analysis, beadchip, section...etc), but when I try to use:
> BLData = readIllumina(arrayNames = metrics$arrayID, textType = ".txt",
> metrics = metrics, backgroundMethod = "none")
> I get this response:
> Found 0 arrays
> Error in seq.default(1, length(tmp), by = 3) : wrong sign in 'by' argument
> I've tried replacing arrayID with Beadchip, since it is used in the
> metrics file, and still it gives me the same message. There should be 24
> arrays. Is there another function to read the arrays in R?
> Thank you in advance,
> Hajar
> 	[[alternative HTML version deleted]]
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