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Series GSE8353 Query DataSets for GSE8353
Status Public on Dec 31, 2007
Title A Mathematical Model for Affymetrix GeneChip Probe Level Data
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Affymetrix GeneChip PM-MM probe pair is designed with the intension of measuring non-specific binding. Though the rationale behind the design id that a PM probe is expected to have a larger value than that of the MM probe, there are many exceptions in actual data. We gave an explanation for this inconsistency based on the assumption of functional states of a gene ‘ON/OFF’. Our hypothesis on PM-MM probe pairs is that the logarithmic of PM and MM values have the same distribution when gene is in OFF state. It means that the probability of MM > PM is expected to be equal to that of MM < PM for OFF genes. The validity of the hypothesis was given by inter-platform comparisons using common targets among three different types of platforms.
Keywords: Affymetrix Gene Chip; Binomial distribution; Mathematical modeling; Oligonucleotide microarray; ON/OFF genes
Overall design Three commercially available single-color oligonucleotide microarray platforms for profiling gene expression - CodeLinkTM Human Whole Genome Bioarray (~55,000 transcripts, GE Healthcare, Tokyo, Japan), Affymetrix GeneChipTM Human Genome U133 Plus 2.0 array (~47,000 transcripts, Affymetrix, Santa Clara, CA), and Agilent Whole Human Genome Oligo Microarray (~41,000 transcripts, Agilent Technologies, Tokyo, Japan), were compared using the same RNA sample extracted from a human neuroblastoma tissue sample.
Contributor(s) Hiyama E, Hiyama K, Ohtaki M, Otani K, Satoh K, Shimamoto T, Mohamad D, Andoh M, Tetsuji T, Kohda M, Okazaki Y, Nishiyama M
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Submission date Jul 02, 2007
Last update date Mar 25, 2019
Contact name Eiso Hiyama
Phone 81822575951
Organization name Hiroshima University
Department Natural Science Center for Basic Research and Deve
Lab LIfe Science
Street address 1-2-3, Kasumi, Minami-ku
City Hiroshima
State/province Hiroshima
ZIP/Postal code 734-8551
Country Japan
Platforms (3)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL2895 GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (3)
GSM205931 Expression analysis of human neuroblastoma (Affymetrix)
GSM206808 Expression analysis of human neuroblastoma (Agilent)
GSM207132 Expression analysis of human neuroblastoma (Codelink)
BioProject PRJNA101369

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8353_RAW.tar 16.5 Mb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table

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