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344 - Southern Methodist University
combine the information in a probe set into one value representing the ... Results: Based on spikein data sets, we compare DFW with several popular methods, via ... Microarray Summarization (FARMS, Hochreiter et al., 2006), is also a model- ...
[ TR344.ashx?la=en - Read/Download File

Summaries of Affymetrix GeneChip probe level data - iSites
summarize probe intensities for each probe set. Several ... MATERIALS AND METHODS. The first ... model and obtain what we refer to as the dChip expression.
[ Irizarry and speed 2003 RMA Nucl Acids Res.pdf - Read/Download File

Affymetrix GeneChips: Quality Control and Normalization
Examine boxplots before and after normalization. 6. 8. 10. 12. 14 raw data. 2. 4. 6 . 8. 10. 12. 14 ... Assume a linear model for the background adjusted normali- zed probe-level ... For each probeset summarize levels of corresponding PM and MM probes to a single .... Selection of methods suitable for a specific investigation.
[ hummel_affy_normalization.pdf?sequence=1 - Read/Download File

Package 'affy' - Bioconductor
This is a class representation for Affymetrix GeneChip probe level data. ... For each probe set computes an expression value using summary.method. .... bg. correct.rma: the model based correction used by the RMA expression measure.
[ affy.pdf - Read/Download File

Package 'affyPLM' - Bioconductor
Fit a Probe Level Model to Affymetrix Genechip Data. .... In particular a probeset summary is normalized using the quantile method and then the probes adjusted  ...
[ affyPLM.pdf - Read/Download File

Analyzing multiple-probe microarray: estimation and application of
Summary: Gene expression index estimation is an essential step in analyzing multiple probe microarray data. Various modeling methods have been proposed in this area. ... set contains 10-20 probe pairs whose expression intensities are measured ... probes do not hold and data transformation techniques can be used to ...
[ MaadooliatHuangHu11.pdf - Read/Download File

Probe-Level Data Analysis of Affymetrix GeneChip Expression Data
Aug 7, 2006 ... Normalization. Summarization ... differences with data analysis techniques. ... Multi-array probe-level model fit to each probeset. ▫ Quality ...
[ Bolstad- AffymetrixTalkAug072006.pdf - Read/Download File

Quality Assessment of Gene Expression Data for Affymetrix
Methods. Quality Assessment of Gene Expression Data for Affymetrix GeneChips. François Collin1 ... probes. We propose some quality assessments derived from fitted models used to ... Summaries of Affymetrix GeneChip probe level data. Nucleic ... we use a virtual median chip constructed by taking, for each probe set, the.
[ 2003_1_QCPoster.pdf - Read/Download File

A Probabilistic Model for the Extraction of Expression Levels from
Affymetrix GeneChip array is an oligonucletide based array technology. ... to a single expression level the probe intensity values for each probe set. The ... Different methods and model have been proposed to summarise probe level data , .... There is no golden standard to compare and test summaries of probe level data.
[ probabilisticOligo.pdf - Read/Download File

Preprocessing High-density Oligonucleotide Arrays - Center for
that are useful for preprocessing Affymetrix GeneChip probe-level data. However, many of the ... and 20 probe pairs, referred to as a probeset, for each gene. ... in Section 2.4 we describe different methods available for summarization. In. Section .... by array, using a global model for the distribution of probe intensities. The.
[ Solutions_ch2.pdf - Read/Download File

A distribution free summarization method for Affymetrix GeneChip
Motivation: Affymetrix GeneChip arrays require summarization in order to combine the ... The raw microarray intensity data are usually highly 'noisy'. Consequently, before ... background corrected intensities of PMs within a probe set after removing the ... 2006), is also a model-based method that uses logarithm - transformed ...
[ Zhongxue_2007_DFW.pdf - Read/Download File

Lecture 7 - jhsph ocw
GeneChip Data. Credit for some ... Affymetrix GeneChip Design. 5'. 3' ... Task: summarize for each probe set the probe level data, i.e., PM and MM pairs, into a single expression measure. ... Li & Wong (2001) fit a model for each probe set, i.e., gene ... Robust regression method to estimate expression measure and. SE from ...
[ lecture7.pdf - Read/Download File

An Expression Index for Affymetrix GeneChips Based - David Rocke
GeneChips is to summarize each of these probe sets into a single expression index ... expression index method GLA, for GLog Average, since after normal- ization at the .... model to the data, as in Durbin and Rocke (2003). This transforma-.
[ ZhouRocke2005.pdf - Read/Download File

PANP – a New Method of Gene Detection on Oligonucleotide
calls on Affymetrix GeneChip® Human Genome Arrays is provided as part ... (MM ) probe data in order to call the resulting probeset present or absent. ... modeling and clustering [1]. ..... standard method to summarize accuracy and make it non-.
[ BIBE07_PANP.pdf - Read/Download File

A systematic statistical linear modeling approach to oligonucleotide
The GeneChip contains probe sets representing unique genes, and each probe set ... This provides 40 times the data compared to traditional summary methods.
[ Oligostat.pdf - Read/Download File

Irizarry et al 2005 - CBS
Results: We benchmarked 31 probe set algorithms using a U95A dataset of spike ... all methods using the same assessment data and summary statistics/ plots.
[ summary_comp_Irizarry_05.pdf - Read/Download File

Exploration, normalization, and summaries of high density
Our analyses make use of three data sets: a small experimental study ... MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index ( MBEI). The exploratory data analyses of the probe level data motivate a new summary ..... Various methods have been proposed for normalizing GeneChip. R.
[ rma.pdf - Read/Download File

Processing of Agilent microRNA array data | SpringerLink
The Agilent microRNA microarray platform interrogates each microRNA with several copies of ... arrays by using a linear model that takes into account the probe affinity effect. ... Therefore we tested the RMA method using probe level data with and ... The dat1 set comprises the microRNA gene expression profiles of bone ...
[ b7x08k649t00057h.pdf - Read/Download File

statistical methods for affymetrix tiling array data - New Prairie Press
Keywords: Microarray; tiling array; differential expression; ANOVA model. 1. Introduction .... 2.4 Summary: Arabidopsis ATH1 Array vs. Tiling 1.0R ... additional data that links probe sets to genes in the current genome annotation version (The .
[ viewcontent.cgi?article=1080&context=agstatconference - Read/Download File

Analysis of probe level patterns in Affymetrix microarray data
May 4, 2007 ... microarray data, including RMA, GCRMA and Model Based Expression Index ( MBEI), summarize ... In Affymetrix arrays, all probes within a probe set should .... The summarization method used is exactly like the RMA method.
[ 1471-2105-8-146.pdf - Read/Download File

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