Hello,

Sorry for the delay in replying. So it seems there is a bug in readIllumina when reading GEO data. In short, we assumed that there are 8 characters before the .tif extension (as happens with data produced by the Illumina scanner). However, as these files come from GEO their format is slightly different. It will take a while to fix, but in the meantime you will be able to read these data using the command.

d <- readIllumina(useImages=FALSE)

This will use the intensities that are already stored in the .txt files which have already been background corrected. For convenience I often use these values anyway as I found Illumina's background correction to be adequate.

Hope this helps,

Mark

-----Original Message-----
From: Fu Sheng [mailto:fusheng66@gmail.com]
Sent: Fri 14/11/2008 23:32
To: Mark Dunning
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] beadarray package question

>
> 2. Can you list the files that are in the working directory where you
> are trying to read from? Each sample should have a _Grn.tif and .txt
> file for a bead-level analysis
>
>
Hello, Mark,

Thank you very much for your quick response. I was thinking readIllumina
would recognize these .tif files by changing tiffExtGrn parameter. Here is
the list of files in working directory:

GSM278088.tif  GSM290551.tif  GSM296419.tif
GSM278088.txt  GSM290551.txt  GSM296419.txt
GSM290549.tif  GSM290552.tif  Illumina_HumanWG-6_V2_0_R1_11223189_A.bgx
GSM290549.txt  GSM290552.txt  Rplots.pdf
GSM290550.tif  GSM296418.tif
GSM290550.txt  GSM296418.txt

Here is error message:

> d<-readIllumina(annoPkg="Humanv2", tiffExtGrn=".tif",
imageManipulation="none", backgroundMethod="none")
Found 0 arrays
Error in seq.default(1, length(tmp), by = 3) :
  wrong sign in 'by' argument
> traceback()
4: stop("wrong sign in 'by' argument")
3: seq.default(1, length(tmp), by = 3)
2: seq(1, length(tmp), by = 3)
1: readIllumina(annoPkg = "Humanv2", tiffExtGrn = ".tif", imageManipulation
= "none",
       backgroundMethod = "none")
> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] beadarray_1.10.0    sma_0.5.15          hwriter_0.93
 [4] geneplotter_1.20.0  annotate_1.20.0     xtable_1.5-4
 [7] AnnotationDbi_1.4.0 lattice_0.17-15     Biobase_2.2.0
[10] limma_2.16.2

loaded via a namespace (and not attached):
[1] DBI_0.2-4          grid_2.8.0         KernSmooth_2.22-22
RColorBrewer_1.0-2
[5] RSQLite_0.7-1

Thank you very much. Have a great weekend!

Yezhou


This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200.
 
This communication and any attachments contain information which is confidential and may also be privileged.   It is for the exclusive use of the intended recipient(s).  If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful.  If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it.
 
E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses.  We do not accept liability for any such matters or their consequences.  Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

	[[alternative HTML version deleted]]

