Navigation Links
Fine Tuning Your Data Analysis:,,, Tunable Parameters of the Affymetrix Expression Analysis Statistical Algorithms

atistical Algorithms work. The examples do not provide sufficient information to serve as guidelines on how to modify parameters for a particular analysis. For most users, Affymetrix recommends using the default values of the tunable parameters as provided in MAS 5.0.

Results


I. Tunable Parameters Affecting Detection

I.A. Calculation and interpretation of Detection p-values

To determine if transcripts are detected specifically, probe pair discrimination scores (R) for every probe set are compared to a threshold value (tau) using a Wilcoxon signedrank test (see references 1 and 2). This non-parametric test establishes whether the probe sets overall discrimination is higher than the threshold, and generates a p-value as a measure of confidence in the specific detection of the transcript (references 1 and 2). The tau threshold influences the actual calculation of p-values, and is discussed further in section I.C. Once p-values are calculated, they can be used to rank probe sets by detection confidence, and to generate qualitative Detection calls. Cutoffs, operating as Figure 2. Modifying alpha1 changes the percentage of probe sets called Present in rat heart RNA (hybridized to the Rat Genome U34A array). The percentage of Present calls is plotted as a function of the user-tunable parameter alpha1. This array's default value for alpha1 (0.04) is indicated with the red line. Changing alpha1 from the default (arrows) alters the analysis stringency and the balance of sensitivity to specificity. tunable parameters, allow the user to modify how the p-values are used to make Detection calls. These are described next.

I.B. Detection Call cutoff values (alphas)

The p-values output by the Detection analysis give rise to three possible Detection Calls: Present (P), Marginal (M), and Absent (A). The calls are g
'"/>

Source:


Page: All 1 2 3 4 5 6 7 8 9 10

Related biology technology :

1. The Affymetrix GeneChip Scanner 3000 New Advances in Scanner Design for Superior Performance, Reliability, and Dynamic Range
2. The New Affymetrix GeneChip Scanner 3000
3. An Epitope Tagging Vector for Gene Expression in Mammalian Cells
4. Antibodies for Studying NMDA Receptor Protein Expression and Synapse-Specific Immunolabeling
5. High-Level Expression of Peanut Allergens Affected by Rare Codon Usage
6. Versatile Vectors for Ponasterone A- Inducible Control of Gene Expression in Mammalian Cells
7. Innovative Tissue Array Technology for High-Throughput Screening of Gene Expression
8. New Mammalian Expression Vectors Employ Stable, High-Level Fluorescence Humanized Renilla GFP Reporter
9. Functional Cloning Using ViraPort Retroviral cDNA Expression Libraries
10. High-Level Protein Expression, One-Column Purification, and FLAG Epitope Tagging in E. coli
11. A New Lambda Vector for Mammalian Expression
Post Your Comments:
(Date:10/20/2014)... , A major pan-European survey into the ... care has revealed changing trends in many important GI ... of healthcare services across the continent. The results of ... (UEG), have been announced today and led to calls ... of GI disorders across Europe ...
(Date:10/20/2014)... N.J. (PRWEB) October 20, 2014 ... the Sidney Kimmel Cancer Center at Thomas Jefferson ... , Through the Strategic Alliance Partnership program, ... OncLive will collaborate to raise awareness of the ... treatment, and other projects. Clinicians and other health ...
(Date:10/19/2014)... The Latin American hardware encryption display market ... with analysis and forecast of revenue. This market was ... to reach $2,366.8 million by 2018, at a CAGR ... the TOC of the Latin American hardware encryption market ... provided. It also provides a glimpse of the segmentation ...
(Date:10/19/2014)... October 19, 2014 The Asia-Pacific ... market in Asia-Pacific with analysis and forecast of ... Asia Pacific Bromine Market report, to get an ... provides a glimpse of the segmentation in the ... tables and figures. , http://www.micromarketmonitor.com/market/asia-pacific-bromine-6741503144.html ...
Breaking Biology Technology:Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 2Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 3Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 4Major Survey Reveals Changing Trends and Inequalities in Healthcare Provision for Gastrointestinal Disorders Across Europe 5Sidney Kimmel Cancer Center at Thomas Jefferson University Partners With OncLive 2Sidney Kimmel Cancer Center at Thomas Jefferson University Partners With OncLive 3The Latin American hardware encryption display market is expected to reach $2,366.8 million by 2018 - New Report by MicroMarket Monitor 2The Latin American hardware encryption display market is expected to reach $2,366.8 million by 2018 - New Report by MicroMarket Monitor 3The Asia-Pacific Bromine Market is estimated to grow to $4,080.1 million by 2018 - New Report by MicroMarket Monitor 2The Asia-Pacific Bromine Market is estimated to grow to $4,080.1 million by 2018 - New Report by MicroMarket Monitor 3
... - The legal wheels still have some spinning to do, ... Foundation not owning three key stem cell patents, or ... decision by United States Patent and Trademark Office ... or modified, but for the first time since University ...
... - What's the penalty for software piracy? Six men who ... Automation software will soon find out as they await sentencing ... for illegally copying the software and selling it on the Internet ... article in the Milwaukee Journal Sentinel . , ,The ...
... presidential primaries less than a year away, campaigns are ... their party's voters. Interestingly, voters are using every available ... reach the polls. , ,This election cycle may be ... and other consumer-generated content. But sifting through all that ...
Cached Biology Technology:Is Wisconsin's stem cell standing diminished? 2Is Wisconsin's stem cell standing diminished? 3Is Wisconsin's stem cell standing diminished? 4Tired of the spin? ExpertVoter website makes candidate selection easier 2Tired of the spin? ExpertVoter website makes candidate selection easier 3
(Date:10/19/2014)... household electricity access in India over the last ... total carbon emissions growth during that time, according ... Nature Climate Change ., "Energy access is ... aspects of life, including education, communication, and health," ... study. , While increased energy access is widely ...
(Date:10/17/2014)... knowledge regarding Ebola is critical and pertinent for practicing ... global outbreak and epidemic. The Journal, Disaster Medicine ... issue, Ebola Virus and Public Health, to surround the ... this critical societal moment. , On October 17, ... Clinicians . The primer was prepared by Dr. Eric ...
(Date:10/16/2014)... constantly wages war on the human body. Battles ... stalemate. In pancreatic cancer, this stalemate—known as tumor ... aggressively malignant, a phenomena that is poorly understood. ... the laboratory of Salvatore Torquato, a Professor of ... conditions surrounding tumor dormancy and the switch to ...
Breaking Biology News(10 mins):Improved electricity access has little impact on climate change 2Modeling tumor dormancy 2
... Head and neck cancer is the sixth most common ... demographic groups, including young women without any known risk factors. ... may increase the movement of precancerous cells in the mouth ... oral cavity. The new results, published in the ...
... adult height may be caused by genetic inheritance, but a ... to be discovered. Now a new meta-analysis of ... over two dozen genes that were not previously associated with ... 30 previously known height genes. "Although the discoveries may not ...
... The hair color of an unknown perpetrator who has ... for forensic investigators. Erasmus MC scientists, in collaboration with their ... predict people,s probable hair color. Their findings will be published ... The research findings demonstrate that on the basis of DNA ...
Cached Biology News:Estrogen may help precancerous cells spread in oral cavity 2CHOP-led study detects dozens of genes for adult height 2CHOP-led study detects dozens of genes for adult height 3Hair color of unknown offenders is no longer a secret 2