[BioC] R command readIllumina with beadarray

[Hajar Hassani Lahsinoui]

Thank you Matt!! That helps!

Hajar

On Oct 4, 2010, at 1:29 AM, Matthew Ritchie wrote:

> 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
> 
> dir(pattern="*perBeadFile.txt")
> 
> If they aren't, change the working directory using the setwd() function.
> 
> Best wishes,
> 
> Matt
> 
>> 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
>> 
>> 
>> 
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>> 
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> 
> 
> 
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