Changes between Version 58 and Version 59 of se.lu.onk.IlluminaSNPNormalization


Ignore:
Timestamp:
May 31, 2021, 2:15:43 PM (3 years ago)
Author:
Jari Häkkinen
Comment:

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  • se.lu.onk.IlluminaSNPNormalization

    v58 v59  
    77=== News ===
    88
    9  * Aug. 25, 2011. Added support for additional beadchips. tQN normalized cluster files for humanOmni2_5M-quad and humanOmniExpress based on Illumina's !HapMap data sets have been released. Download cluster files for [http://cbbp.thep.lu.se/~markus/software/tQN/humanOmni2_5M-quad_tQN_clusters.zip?format=raw humanOmni2_5M-quad] and [http://cbbp.thep.lu.se/~markus/software/tQN/humanOmniExpress_tQN_clusters.zip?format=raw humanOmniExpress]. See special note for these platforms under download tQN below.
     9 * Aug. 25, 2011. Added support for additional beadchips. tQN normalized cluster files for humanOmni2_5M-quad and humanOmniExpress based on Illumina's !HapMap data sets have been released. Download cluster files for [attachment:humanOmni2_5M-quad_tQN_clusters.zip?format=raw humanOmni2_5M-quad] and [attachment:humanOmniExpress_tQN_clusters.zip?format=raw humanOmniExpress]. See special note for these platforms under download tQN below.
    1010
    1111
    12  * Sept. 29, 2009. Added support for additional beadchip. tQN normalized cluster file for human1M-omnia based on Illumina's !HapMap data set has been released. Download [http://cbbp.thep.lu.se/~markus/software/tQN/human1M-omnia_tQN_clusters.zip?format=raw here].
     12 * Sept. 29, 2009. Added support for additional beadchip. tQN normalized cluster file for human1M-omnia based on Illumina's !HapMap data set has been released. Download [attachment:human1M-omnia_tQN_clusters.zip?format=raw here].
    1313
    14  * Sept. 11, 2009. Added support for additional beadchip. tQN normalized cluster file for human660w-quad based on Illumina's !HapMap data set has been released. Download [http://cbbp.thep.lu.se/~markus/software/tQN/human660w-quad_tQN_clusters.zip?format=raw here].
     14 * Sept. 11, 2009. Added support for additional beadchip. tQN normalized cluster file for human660w-quad based on Illumina's !HapMap data set has been released. Download [attachment:human660w-quad_tQN_clusters.zip?format=raw here].
    1515
    1616 * Mar. 13, 2009. tQN 1.1.2 released. This is a minor bug-fix release. 'split_samples.pl' has been modified to replace commas (,) with points(.) in data columns as !BeadStudio exports data with commas for some language settings, which caused problems for tQN.
    … …  
    3535=== Download tQN ===
    3636
    37 [http://cbbp.thep.lu.se/~markus/software/tQN/tQN-1.1.2.zip?format=raw Download the latest stand-alone release (tQN-1.1.2)]. This release includes tQN cluster files for humanhap300, humanhap300-duo, humancnv370-duo, humancnv370-quad, humanhap550, human610-quad, and human1M-duo.
     37[attachment:tQN-1.1.2.zip?format=raw Download the latest stand-alone release (tQN-1.1.2)]. This release includes tQN cluster files for humanhap300, humanhap300-duo, humancnv370-duo, humancnv370-quad, humanhap550, human610-quad, and human1M-duo.
    3838
    39 [http://cbbp.thep.lu.se/~markus/software/tQN/human660w-quad_tQN_clusters.zip?format=raw Download tQN cluster file for human660w-quad]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with human660w-quad beadchips. 
     39[attachment:human660w-quad_tQN_clusters.zip?format=raw Download tQN cluster file for human660w-quad]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with human660w-quad beadchips. 
    4040
    41 [http://cbbp.thep.lu.se/~markus/software/tQN/human1M-omnia_tQN_clusters.zip?format=raw Download tQN cluster file for human1M-omnia]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with human1M-omnia beadchips.   
     41[attachment:human1M-omnia_tQN_clusters.zip?format=raw Download tQN cluster file for human1M-omnia]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with human1M-omnia beadchips.   
    4242
    43 [http://cbbp.thep.lu.se/~markus/software/tQN/humanOmni2_5M-quad_tQN_clusters.zip?format=raw Download tQN cluster file for humanOmni2_5M-quad]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with humanOmni2_5-quad beadchips. Special note: We have observed considerable assymetry in BAF estimates with this platform. In our experience tQN improves data from this platform but not to the same extent as with earlier beadchips.   
     43[attachment:humanOmni2_5M-quad_tQN_clusters.zip?format=raw Download tQN cluster file for humanOmni2_5M-quad]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with humanOmni2_5-quad beadchips. Special note: We have observed considerable assymetry in BAF estimates with this platform. In our experience tQN improves data from this platform but not to the same extent as with earlier beadchips.   
    4444
    45 [http://cbbp.thep.lu.se/~markus/software/tQN/humanOmniExpress_tQN_clusters.zip?format=raw Download tQN cluster file for humanOmniExpress]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with humanOmniExpress beadchips. Special note: We have observed considerable assymetry in BAF estimates with this platform. In our experience tQN improves data from this platform but not to the same extent as with earlier beadchips.   
     45[attachment:humanOmniExpress_tQN_clusters.zip?format=raw Download tQN cluster file for humanOmniExpress]. This additional cluster file is not part of the tQN-1.1.2 release. Unzip and put the resulting txt-file in the subdirectory ''lib'' in your tQN installation if you want to use tQN with humanOmniExpress beadchips. Special note: We have observed considerable assymetry in BAF estimates with this platform. In our experience tQN improves data from this platform but not to the same extent as with earlier beadchips.   
    4646
    4747=== Supplemental data ===
    … …  
    109109''tQN B allele frequencies and log R ratios''
    110110
    111   CNV probes are not normalized by tQN; for these probes the original X and Y intensities from !BeadStudio are kept. tQN may result in a slightly smaller number of SNPs having data. The reason for this reduction is that some SNPs have not been genotyped in the !HapMap samples used to generate the cluster files. A detailed description of how tQN X and Y intensities are turned into tQN BAF and tQN log R ratios is available [http://cbbp.thep.lu.se/~markus/software/tQN/ReadMe_calculation_BAF_Log_R_Ratio.pdf?format=raw here].
     111  CNV probes are not normalized by tQN; for these probes the original X and Y intensities from !BeadStudio are kept. tQN may result in a slightly smaller number of SNPs having data. The reason for this reduction is that some SNPs have not been genotyped in the !HapMap samples used to generate the cluster files. A detailed description of how tQN X and Y intensities are turned into tQN BAF and tQN log R ratios is available [attachment:ReadMe_calculation_BAF_Log_R_Ratio.pdf?format=raw here].
    112112
    113113''Supported beadchip types''