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| 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
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| 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
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| 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.
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| 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 |
| Citation missing |
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| Submission date |
Jul 02, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Eiso Hiyama |
| E-mail(s) |
eiso@hiroshima-u.ac.jp
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| Phone |
81822575951
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| Organization name |
Hiroshima University
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| Department |
Natural Science Center for Basic Research and Deve
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| Lab |
LIfe Science
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| Street address |
1-2-3, Kasumi, Minami-ku
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| City |
Hiroshima |
| State/province |
Hiroshima |
| ZIP/Postal code |
734-8551 |
| Country |
Japan |
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| 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) |
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| Samples (3) |
| GSM205931 |
Expression analysis of human neuroblastoma (Affymetrix) |
| GSM206808 |
Expression analysis of human neuroblastoma (Agilent) |
| GSM207132 |
Expression analysis of human neuroblastoma (Codelink) |
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| Relations |
| BioProject |
PRJNA101369 |
| 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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