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.

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]]