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Sample GSM123153 Query DataSets for GSM123153
Status Public on Sep 08, 2006
Title MAQC_GEH_2_C2
Sample type RNA
 
Source name MAQC sample C, i.e., MAQC samples A and B mixed at 75%:25% ratio (A:B).
Organism Homo sapiens
Characteristics NA

Extracted molecule total RNA
Label biotin
Label protocol MAQC total RNA samples were processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol (Please refer to CodeLink(TM) iExpress Expression Assay Regent Kit Technical Manual for details at www.codelinkbioarrays.com) and hybridized to CodeLink(TM) Human Whole Genome bioarrays (catalog #300026).
 
Scan protocol All arrays were scanned on the GenePix 4000B scanner using manufacturer recommended settings of 600 PMT, 100% laser power, and 5 micron resolution.
Description NA
Data processing The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics. These quality metrics are applied to each spot and are displayed both numerically and as a qualitative assignment. In the MAQC study, for all microarray platforms, genes which were not detected (i.e., 'absent') were excluded from subsequent analyses. The spots which are below noise on the GE Healthcare platform are flagged by the software package as 'L' and represent cases where the spot mean intensity is less than local background median plus 1.5 standard deviations of local background. Details on the CodeLink(TM) detection algorithms can be found at the www.codelinkbioarrays.com (http://www1.amershambiosciences.com/APTRIX/upp00919.nsf/Content/WD%3AImproved+method%28275651129-B500%29?OpenDocument&hometitle=WebDocs).
 
Submission date Jul 25, 2006
Last update date Aug 14, 2006
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL2895
Series (1)
GSE5350 MicroArray Quality Control (MAQC) Project

Data table header descriptions
ID_REF Manufacturer's 'Feature_id'
VALUE Local background subtracted intensity data after median-scaling each array to a median of 1.
Flag_Detection GEH's original flag information ('Quality_flag') is provided: G = 'Good', L = 'Absent', S = 'Saturated', M = 'Manufacturing Defect', I = 'Irregular Shape', C = 'Contaminated Spot'.

Data table
ID_REF VALUE Flag_Detection
1001 104.4188 G
1002 7.3421 G
1003 -0.0068 L
1004 -0.0125 L
1005 0.0388 L
1006 0.3153 G
1007 0.3648 G
1008 99.6083 G
1009 2.0614 G
1010 3.8384 G
1011 0.4744 G
1012 3.7577 G
1013 0.3555 G
1014 0.0547 L
1015 98.8292 G
1016 0.6038 G
1017 0.3208 G
1018 0.1886 L
1019 0.0298 L
1020 -0.0318 L

Total number of rows: 54359

Table truncated, full table size 838 Kbytes.




Supplementary file Size Download File type/resource
GSM123153_GEH_2_C2.TXT.gz 7.2 Mb (ftp)(http) TXT

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