Hi Anna,

I'm afraid if those are the only files that were generated then you are
unable to do a bead-level analysis.  Without the perBeadFile.txt files (and
optionally the tiff files) I'm afraid you're limited to using Illumina's
summarized values. The jpg files may be useful to view in your favourite
image viewer, just to see if there's anything obviously weird on an array
surface that corroborates outlying values on a between-array scale, but the
tools for localised artifact detection and removal and alternative
summarization methods rely on on the full bead-level data.

Sorry that's not of more help,

Mike

On 11 April 2012 01:19, Anna [guest] <guest@bioconductor.org> wrote:

>
> Hi,
>
> I am interested in using the beadarray package to process the raw data
> generated by the Illumnia's iScan.  Unfortunately,  the settings for the
> Illumina's iScan was not set correctly during the run to output the
> perBeadFile.txt files.  The following files were generated from the run:
>
> 5456816021_qc.txt
> 5456816021_R01C01_1_Focus_scan#1_swath#1_point#1_try#1.jpg
> 5456816021_R01C01_1-Swath1_Grn.jpg
> 5456816021_R01C01_1-Swath1_Red.jpg
> 5456816021_R01C01_1-Swath2_Grn.jpg
> 5456816021_R01C01_1-Swath2_Red.jpg
> 5456816021_R01C01_1.xml
> 5456816021_R01C01_2_Focus_scan#1_swath#1_point#1_try#1.jpg
> 5456816021_R01C01_2-Swath1_Grn.jpg
> 5456816021_R01C01_2-Swath1_Red.jpg
> 5456816021_R01C01_2-Swath2_Grn.jpg
> 5456816021_R01C01_2-Swath2_Red.jpg
> 5456816021_R01C01_2.xml
>
> Is it still possible to use beadarray to analyze the raw data outputs from
> the iScan?  Thanks in advance for any help.
>
> Anna
>
>  -- output of sessionInfo():
>
> R version 2.15.0 (2012-03-30)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

	[[alternative HTML version deleted]]

