Hi Anna, I think there's some confusion as to the types (and names) of the files that can be generated by the scanner. The default is to generate summarized data for each bead type. These are stored in the .idat files. However you can also set the scanner to produce files with the suffix _beadTypeFile.txt, which store the same summary information but in the format shown in the Biostar post you found. However, this is still summarized data for each bead type. Optionally you can set the scanner to produce bead-level information. They will be written to files with the suffix _perBeadFile.txt. Choosing to create these has to be done at the time the array is to be scanned. If they are not then there is no way to generate them from the summary data. I'm afraid looking the list of files you've provided you cannot do a bead-level analysis. You can either scan the arrays again with the bead-level output options turned on, or proceed using the summarized values. I hope that clears things up a little, Mike On 12 April 2012 20:53, <bzguan@ucdavis.edu> wrote: > > Hi Mike, > > Sorry, below is actually the complete list of all the files that were > generated. > > I found a post on Biostar ( > http://www.biostars.org/post/show/12602/read-illumina-iscan-data- > directly-into-r-using-/) by someone with a similar problem as me. One of > the response by Lars > Gidskehaug states, "If the scanner has not been set to produce such > summary files, the > bioconductor package beadarray can be used to create the files. " > Currently, I have been trying to > figure out how to use beadarray to generate the perBEADfile.txt files from > the files below. Are you > saying that it is not possible to generate the perBEADfile.txt files using > beadarray? > > Anna > > > Human660W-Quad_v1_H.bpm > Human660W-Quad_v1_H.egt > 5456816013_qc.txt > 5456816013_R01C01_1_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_1-Swath1_Grn.jpg > 5456816013_R01C01_1-Swath1_Red.jpg > 5456816013_R01C01_1-Swath2_Grn.jpg > 5456816013_R01C01_1-Swath2_Red.jpg > 5456816013_R01C01_1.xml > 5456816013_R01C01_2_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_2-Swath1_Grn.jpg > 5456816013_R01C01_2-Swath1_Red.jpg > 5456816013_R01C01_2-Swath2_Grn.jpg > 5456816013_R01C01_2-Swath2_Red.jpg > 5456816013_R01C01_2.xml > 5456816013_R01C01_3_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_3-Swath1_Grn.jpg > 5456816013_R01C01_3-Swath1_Red.jpg > 5456816013_R01C01_3-Swath2_Grn.jpg > 5456816013_R01C01_3-Swath2_Red.jpg > 5456816013_R01C01_3.xml > 5456816013_R01C01_4_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_4-Swath1_Grn.jpg > 5456816013_R01C01_4-Swath1_Red.jpg > 5456816013_R01C01_4-Swath2_Grn.jpg > 5456816013_R01C01_4-Swath2_Red.jpg > 5456816013_R01C01_4.xml > 5456816013_R01C01_5_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_5-Swath1_Grn.jpg > 5456816013_R01C01_5-Swath1_Red.jpg > 5456816013_R01C01_5-Swath2_Grn.jpg > 5456816013_R01C01_5-Swath2_Red.jpg > 5456816013_R01C01_5.xml > 5456816013_R01C01_6_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_6-Swath1_Grn.jpg > 5456816013_R01C01_6-Swath1_Red.jpg > 5456816013_R01C01_6-Swath2_Grn.jpg > 5456816013_R01C01_6-Swath2_Red.jpg > 5456816013_R01C01_6.xml > 5456816013_R01C01_7_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_7-Swath1_Grn.jpg > 5456816013_R01C01_7-Swath1_Red.jpg > 5456816013_R01C01_7-Swath2_Grn.jpg > 5456816013_R01C01_7-Swath2_Red.jpg > 5456816013_R01C01_7.xml > 5456816013_R01C01_8_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_8-Swath1_Grn.jpg > 5456816013_R01C01_8-Swath1_Red.jpg > 5456816013_R01C01_8-Swath2_Grn.jpg > 5456816013_R01C01_8-Swath2_Red.jpg > 5456816013_R01C01_8.xml > 5456816013_R01C01_9_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_9-Swath1_Grn.jpg > 5456816013_R01C01_9-Swath1_Red.jpg > 5456816013_R01C01_9-Swath2_Grn.jpg > 5456816013_R01C01_9-Swath2_Red.jpg > 5456816013_R01C01_9.xml > 5456816013_R01C01_10_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_10-Swath1_Grn.jpg > 5456816013_R01C01_10-Swath1_Red.jpg > 5456816013_R01C01_10-Swath2_Grn.jpg > 5456816013_R01C01_10-Swath2_Red.jpg > 5456816013_R01C01_10.xml > 5456816013_R01C01_11_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_11-Swath1_Grn.jpg > 5456816013_R01C01_11-Swath1_Red.jpg > 5456816013_R01C01_11-Swath2_Grn.jpg > 5456816013_R01C01_11-Swath2_Red.jpg > 5456816013_R01C01_11.xml > 5456816013_R01C01_12_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C01_12-Swath1_Grn.jpg > 5456816013_R01C01_12-Swath1_Red.jpg > 5456816013_R01C01_12-Swath2_Grn.jpg > 5456816013_R01C01_12-Swath2_Red.jpg > 5456816013_R01C01_12.xml > 5456816013_R01C01_Grn.idat > 5456816013_R01C01_Red.idat > 5456816013_R01C02_1_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_1-Swath1_Grn.jpg > 5456816013_R01C02_1-Swath1_Red.jpg > 5456816013_R01C02_1-Swath2_Grn.jpg > 5456816013_R01C02_1-Swath2_Red.jpg > 5456816013_R01C02_1.xml > 5456816013_R01C02_2_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_2-Swath1_Grn.jpg > 5456816013_R01C02_2-Swath1_Red.jpg > 5456816013_R01C02_2-Swath2_Grn.jpg > 5456816013_R01C02_2-Swath2_Red.jpg > 5456816013_R01C02_2.xml > 5456816013_R01C02_3_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_3-Swath1_Grn.jpg > 5456816013_R01C02_3-Swath1_Red.jpg > 5456816013_R01C02_3-Swath2_Grn.jpg > 5456816013_R01C02_3-Swath2_Red.jpg > 5456816013_R01C02_3.xml > 5456816013_R01C02_4_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_4-Swath1_Grn.jpg > 5456816013_R01C02_4-Swath1_Red.jpg > 5456816013_R01C02_4-Swath2_Grn.jpg > 5456816013_R01C02_4-Swath2_Red.jpg > 5456816013_R01C02_4.xml > 5456816013_R01C02_5_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_5-Swath1_Grn.jpg > 5456816013_R01C02_5-Swath1_Red.jpg > 5456816013_R01C02_5-Swath2_Grn.jpg > 5456816013_R01C02_5-Swath2_Red.jpg > 5456816013_R01C02_5.xml > 5456816013_R01C02_6_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_6-Swath1_Grn.jpg > 5456816013_R01C02_6-Swath1_Red.jpg > 5456816013_R01C02_6-Swath2_Grn.jpg > 5456816013_R01C02_6-Swath2_Red.jpg > 5456816013_R01C02_6.xml > 5456816013_R01C02_7_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_7-Swath1_Grn.jpg > 5456816013_R01C02_7-Swath1_Red.jpg > 5456816013_R01C02_7-Swath2_Grn.jpg > 5456816013_R01C02_7-Swath2_Red.jpg > 5456816013_R01C02_7.xml > 5456816013_R01C02_8_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_8-Swath1_Grn.jpg > 5456816013_R01C02_8-Swath1_Red.jpg > 5456816013_R01C02_8-Swath2_Grn.jpg > 5456816013_R01C02_8-Swath2_Red.jpg > 5456816013_R01C02_8.xml > 5456816013_R01C02_9_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_9-Swath1_Grn.jpg > 5456816013_R01C02_9-Swath1_Red.jpg > 5456816013_R01C02_9-Swath2_Grn.jpg > 5456816013_R01C02_9-Swath2_Red.jpg > 5456816013_R01C02_9.xml > 5456816013_R01C02_10_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_10-Swath1_Grn.jpg > 5456816013_R01C02_10-Swath1_Red.jpg > 5456816013_R01C02_10-Swath2_Grn.jpg > 5456816013_R01C02_10-Swath2_Red.jpg > 5456816013_R01C02_10.xml > 5456816013_R01C02_11_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_11-Swath1_Grn.jpg > 5456816013_R01C02_11-Swath1_Red.jpg > 5456816013_R01C02_11-Swath2_Grn.jpg > 5456816013_R01C02_11-Swath2_Red.jpg > 5456816013_R01C02_11.xml > 5456816013_R01C02_12_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R01C02_12-Swath1_Grn.jpg > 5456816013_R01C02_12-Swath1_Red.jpg > 5456816013_R01C02_12-Swath2_Grn.jpg > 5456816013_R01C02_12-Swath2_Red.jpg > 5456816013_R01C02_12.xml > 5456816013_R01C02_Grn.idat > 5456816013_R01C02_Red.idat > 5456816013_R02C01_1_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_1-Swath1_Grn.jpg > 5456816013_R02C01_1-Swath1_Red.jpg > 5456816013_R02C01_1-Swath2_Grn.jpg > 5456816013_R02C01_1-Swath2_Red.jpg > 5456816013_R02C01_1.xml > 5456816013_R02C01_2_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_2-Swath1_Grn.jpg > 5456816013_R02C01_2-Swath1_Red.jpg > 5456816013_R02C01_2-Swath2_Grn.jpg > 5456816013_R02C01_2-Swath2_Red.jpg > 5456816013_R02C01_2.xml > 5456816013_R02C01_3_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_3-Swath1_Grn.jpg > 5456816013_R02C01_3-Swath1_Red.jpg > 5456816013_R02C01_3-Swath2_Grn.jpg > 5456816013_R02C01_3-Swath2_Red.jpg > 5456816013_R02C01_3.xml > 5456816013_R02C01_4_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_4-Swath1_Grn.jpg > 5456816013_R02C01_4-Swath1_Red.jpg > 5456816013_R02C01_4-Swath2_Grn.jpg > 5456816013_R02C01_4-Swath2_Red.jpg > 5456816013_R02C01_4.xml > 5456816013_R02C01_5_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_5-Swath1_Grn.jpg > 5456816013_R02C01_5-Swath1_Red.jpg > 5456816013_R02C01_5-Swath2_Grn.jpg > 5456816013_R02C01_5-Swath2_Red.jpg > 5456816013_R02C01_5.xml > 5456816013_R02C01_6_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_6-Swath1_Grn.jpg > 5456816013_R02C01_6-Swath1_Red.jpg > 5456816013_R02C01_6-Swath2_Grn.jpg > 5456816013_R02C01_6-Swath2_Red.jpg > 5456816013_R02C01_6.xml > 5456816013_R02C01_7_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_7-Swath1_Grn.jpg > 5456816013_R02C01_7-Swath1_Red.jpg > 5456816013_R02C01_7-Swath2_Grn.jpg > 5456816013_R02C01_7-Swath2_Red.jpg > 5456816013_R02C01_7.xml > 5456816013_R02C01_8_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_8-Swath1_Grn.jpg > 5456816013_R02C01_8-Swath1_Red.jpg > 5456816013_R02C01_8-Swath2_Grn.jpg > 5456816013_R02C01_8-Swath2_Red.jpg > 5456816013_R02C01_8.xml > 5456816013_R02C01_9_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_9-Swath1_Grn.jpg > 5456816013_R02C01_9-Swath1_Red.jpg > 5456816013_R02C01_9-Swath2_Grn.jpg > 5456816013_R02C01_9-Swath2_Red.jpg > 5456816013_R02C01_9.xml > 5456816013_R02C01_10_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_10-Swath1_Grn.jpg > 5456816013_R02C01_10-Swath1_Red.jpg > 5456816013_R02C01_10-Swath2_Grn.jpg > 5456816013_R02C01_10-Swath2_Red.jpg > 5456816013_R02C01_10.xml > 5456816013_R02C01_11_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_11-Swath1_Grn.jpg > 5456816013_R02C01_11-Swath1_Red.jpg > 5456816013_R02C01_11-Swath2_Grn.jpg > 5456816013_R02C01_11-Swath2_Red.jpg > 5456816013_R02C01_11.xml > 5456816013_R02C01_12_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C01_12-Swath1_Grn.jpg > 5456816013_R02C01_12-Swath1_Red.jpg > 5456816013_R02C01_12-Swath2_Grn.jpg > 5456816013_R02C01_12-Swath2_Red.jpg > 5456816013_R02C01_12.xml > 5456816013_R02C01_Grn.idat > 5456816013_R02C01_Red.idat > 5456816013_R02C02_1_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_1-Swath1_Grn.jpg > 5456816013_R02C02_1-Swath1_Red.jpg > 5456816013_R02C02_1-Swath2_Grn.jpg > 5456816013_R02C02_1-Swath2_Red.jpg > 5456816013_R02C02_1.xml > 5456816013_R02C02_2_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_2-Swath1_Grn.jpg > 5456816013_R02C02_2-Swath1_Red.jpg > 5456816013_R02C02_2-Swath2_Grn.jpg > 5456816013_R02C02_2-Swath2_Red.jpg > 5456816013_R02C02_2.xml > 5456816013_R02C02_3_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_3-Swath1_Grn.jpg > 5456816013_R02C02_3-Swath1_Red.jpg > 5456816013_R02C02_3-Swath2_Grn.jpg > 5456816013_R02C02_3-Swath2_Red.jpg > 5456816013_R02C02_3.xml > 5456816013_R02C02_4_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_4-Swath1_Grn.jpg > 5456816013_R02C02_4-Swath1_Red.jpg > 5456816013_R02C02_4-Swath2_Grn.jpg > 5456816013_R02C02_4-Swath2_Red.jpg > 5456816013_R02C02_4.xml > 5456816013_R02C02_5_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_5-Swath1_Grn.jpg > 5456816013_R02C02_5-Swath1_Red.jpg > 5456816013_R02C02_5-Swath2_Grn.jpg > 5456816013_R02C02_5-Swath2_Red.jpg > 5456816013_R02C02_5.xml > 5456816013_R02C02_6_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_6-Swath1_Grn.jpg > 5456816013_R02C02_6-Swath1_Red.jpg > 5456816013_R02C02_6-Swath2_Grn.jpg > 5456816013_R02C02_6-Swath2_Red.jpg > 5456816013_R02C02_6.xml > 5456816013_R02C02_7_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_7-Swath1_Grn.jpg > 5456816013_R02C02_7-Swath1_Red.jpg > 5456816013_R02C02_7-Swath2_Grn.jpg > 5456816013_R02C02_7-Swath2_Red.jpg > 5456816013_R02C02_7.xml > 5456816013_R02C02_8_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_8-Swath1_Grn.jpg > 5456816013_R02C02_8-Swath1_Red.jpg > 5456816013_R02C02_8-Swath2_Grn.jpg > 5456816013_R02C02_8-Swath2_Red.jpg > 5456816013_R02C02_8.xml > 5456816013_R02C02_9_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_9-Swath1_Grn.jpg > 5456816013_R02C02_9-Swath1_Red.jpg > 5456816013_R02C02_9-Swath2_Grn.jpg > 5456816013_R02C02_9-Swath2_Red.jpg > 5456816013_R02C02_9.xml > 5456816013_R02C02_10_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_10-Swath1_Grn.jpg > 5456816013_R02C02_10-Swath1_Red.jpg > 5456816013_R02C02_10-Swath2_Grn.jpg > 5456816013_R02C02_10-Swath2_Red.jpg > 5456816013_R02C02_10.xml > 5456816013_R02C02_11_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_11-Swath1_Grn.jpg > 5456816013_R02C02_11-Swath1_Red.jpg > 5456816013_R02C02_11-Swath2_Grn.jpg > 5456816013_R02C02_11-Swath2_Red.jpg > 5456816013_R02C02_11.xml > 5456816013_R02C02_12_Focus_scan#1_swath#1_point#1_try#1.jpg > 5456816013_R02C02_12-Swath1_Grn.jpg > 5456816013_R02C02_12-Swath1_Red.jpg > 5456816013_R02C02_12-Swath2_Grn.jpg > 5456816013_R02C02_12-Swath2_Red.jpg > 5456816013_R02C02_12.xml > 5456816013_R02C02_Grn.idat > 5456816013_R02C02_Red.idat > 5456816013.sdf > AutoCenter_focus_fiducial#1_alt#1.jpg > AutoCenter_focus_fiducial#2_alt#1.jpg > AutoCenter_focus_fiducial#3_alt#1.jpg > AutoTilt_focus_fiducial#1_alt#1_focus#1_old0.jpg > AutoTilt_focus_fiducial#1_alt#1_focus#1.jpg > AutoTilt_focus_fiducial#2_alt#1_focus#1_old0.jpg > AutoTilt_focus_fiducial#2_alt#1_focus#1.jpg > AutoTilt_focus_fiducial#3_alt#1_focus#1_old0.jpg > AutoTilt_focus_fiducial#3_alt#1_focus#1.jpg > Effective.cfg > Metrics.txt > > > > 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 > > > -- Mike Smith PhD Student Computational Biology Group Cambridge University [[alternative HTML version deleted]]