Rafael A.Irizarry, Bridget Hobbs, Francois Collin, Yasmin D. Beazer-Barclay, Kristen J.Antonellis, Uwe Scherf and Terence P.Speed
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Biostatistics 4:249-264 (2003)
[PDF][Web Site]
・GeneChipの包括的調査(RMAの性能を検証?)。
・データ
1.a small experimental study consisting of five MGU74A mouse GeneChip arrays
2. part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip arrays
3. part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip arrays
・発現量指標(summary measures)
1. average difference(AvDiff)
2. MAS 5.0
3. Li and Wong multiplicative model-based expression index (MBEI)
4. robust multi-array average (RMA)
・概要「In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip? system with the objective of improving upon cyrrently used measures of gene expression.」
・RMA「To summarize, in this paper we consider a new expression measure that (i) background-corrects the arrays using the transformation B(・), (ii) normalization the arrays using quantile normalization , and (iii) for each probe set n, fits a linear model (2) to the background-corrected, normalized and log (base 2) transformed probe intensities」
・「The advantage of RMA is especially noticeable in the low expression values where the SD is 10 times smaller than the other measures.」
・結論「We conclude that there is no obvious downside to summarizing the expression level of a probe set with RMA, and attaching an SE to this quantity using a linear model that removes probe-specific affinities.」
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Biostatistics 4:249-264 (2003)
[PDF][Web Site]
・GeneChipの包括的調査(RMAの性能を検証?)。
・データ
1.a small experimental study consisting of five MGU74A mouse GeneChip arrays
2. part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip arrays
3. part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip arrays
・発現量指標(summary measures)
1. average difference(AvDiff)
2. MAS 5.0
3. Li and Wong multiplicative model-based expression index (MBEI)
4. robust multi-array average (RMA)
・概要「In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip? system with the objective of improving upon cyrrently used measures of gene expression.」
・RMA「To summarize, in this paper we consider a new expression measure that (i) background-corrects the arrays using the transformation B(・), (ii) normalization the arrays using quantile normalization , and (iii) for each probe set n, fits a linear model (2) to the background-corrected, normalized and log (base 2) transformed probe intensities」
・「The advantage of RMA is especially noticeable in the low expression values where the SD is 10 times smaller than the other measures.」
・結論「We conclude that there is no obvious downside to summarizing the expression level of a probe set with RMA, and attaching an SE to this quantity using a linear model that removes probe-specific affinities.」