Difference: ProteomicsBioLab (1 vs. 11)

Revision 11
02 Oct 2014 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Deleted:
<
<
Medical Bioinformatics

 

Back to menu
Line: 15 to 14
 
We have been involved in the experimental design and analysis of several SELDI-TOF proteomics experiments. Typically, the different steps in our analysis approach are
Changed:
<
<
  • experimental design: sample size, randomization of samples across multiple conditions
>
>
  • experimental design: sample size, randomization of samples
 
  • quality control (QC): variety of QC plots and quantitative measures to aid in detecting problematic samples
  • pre-processing: smoothing, baseline correction, normalization, alignment, peak detection and quantification
  • unsupervised analysis: for example, using clustering and principal component analysis
Revision 10
21 Mar 2011 - Main.AngelaLuijf
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Changed:
<
<
>
>
 
Back to menuSort

Changed:
<
<
Proteomics analysis People
>
>
Proteomics analysis People
 

Line: 25 to 26
 
    • cross-validation on the training data to determine optimal values for hyperparameters of a model and to select features

Changed:
<
<
>
>
 .
Changed:
<
<
>
>
 
Selected publications
BC van Munster, MJ van Breemen, PD Moerland, D Speijer, SE de Rooij, CJG Pfrommer, M Levi, MW Hollmann, JM Aerts, AH Zwinderman, JC Korevaar (2009). Proteomic profiling of plasma and serum of elderly patients with postoperative delirium. Journal of Neuropsychiatry and Clinical Neurosciences, 21:284-91. PubMed
W Wegdam*, PD Moerland*, MR Buist, E Ver Loren van Themaat, B Bleijlevens, HCJ Hoefsloot, CG de Koster, JMFG Aerts (2009). Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Science, 7:19. PubMed *Contributed equally \ No newline at end of file
Revision 9
31 Jan 2010 - Main.AntoineVanKampen
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Line: 28 to 28
 
Added:
>
>
 .
Revision 8
24 Jan 2010 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Line: 17 to 17
 
  • experimental design: sample size, randomization of samples across multiple conditions
  • quality control (QC): variety of QC plots and quantitative measures to aid in detecting problematic samples
  • pre-processing: smoothing, baseline correction, normalization, alignment, peak detection and quantification
Added:
>
>
  • unsupervised analysis: for example, using clustering and principal component analysis
 
  • differential expression: detection of differentially expressed proteins for a variety of experimental designs (multiple groups, time series, inclusion of covariates, regression), emperical Bayes, correction for multiple testing, permutation tests
  • classification: using a variety of statistical and machine learning models (discriminant analysis, decision trees, logistic regression, nearest centroid, support vector machines, neural networks, ...) in a double cross-validation scheme
    • complete separation of training data used for estimating the parameters of a model and test data for estimating the accuracy of the model
Revision 7
23 Jan 2010 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Line: 10 to 10
 
Proteomics analysis People
Added:
>
>
 
Changed:
<
<
Under construction
>
>
We have been involved in the experimental design and analysis of several SELDI-TOF proteomics experiments. Typically, the different steps in our analysis approach are

  • experimental design: sample size, randomization of samples across multiple conditions
  • quality control (QC): variety of QC plots and quantitative measures to aid in detecting problematic samples
  • pre-processing: smoothing, baseline correction, normalization, alignment, peak detection and quantification
  • differential expression: detection of differentially expressed proteins for a variety of experimental designs (multiple groups, time series, inclusion of covariates, regression), emperical Bayes, correction for multiple testing, permutation tests
  • classification: using a variety of statistical and machine learning models (discriminant analysis, decision trees, logistic regression, nearest centroid, support vector machines, neural networks, ...) in a double cross-validation scheme
    • complete separation of training data used for estimating the parameters of a model and test data for estimating the accuracy of the model
    • multiple estimates of classification accuracy to be able to assess its variance
    • cross-validation on the training data to determine optimal values for hyperparameters of a model and to select features
 
Line: 19 to 29
 .
\ No newline at end of file
Added:
>
>

Selected publications
BC van Munster, MJ van Breemen, PD Moerland, D Speijer, SE de Rooij, CJG Pfrommer, M Levi, MW Hollmann, JM Aerts, AH Zwinderman, JC Korevaar (2009). Proteomic profiling of plasma and serum of elderly patients with postoperative delirium. Journal of Neuropsychiatry and Clinical Neurosciences, 21:284-91. PubMed
W Wegdam*, PD Moerland*, MR Buist, E Ver Loren van Themaat, B Bleijlevens, HCJ Hoefsloot, CG de Koster, JMFG Aerts (2009). Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets. Proteome Science, 7:19. PubMed *Contributed equally
Revision 6
22 Jan 2010 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Line: 15 to 15
 
Changed:
<
<
>
>
 .
Revision 5
22 Dec 2009 - Main.AntoineVanKampen
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Line: 6 to 6
 
Back to menuSort

Changed:
<
<
Proteomics analysis
>
>
Proteomics analysis People
  Under construction \ No newline at end of file
Added:
>
>
.
Revision 4
21 Dec 2009 - Main.AntoineVanKampen
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Medical Bioinformatics

Line: 6 to 6
 
Back to menuSort

Changed:
<
<
Proteomics analysis
>
>
Proteomics analysis
 
Deleted:
<
<
  Under construction \ No newline at end of file
Revision 3
19 Dec 2009 - Main.AntoineVanKampen
Line: 1 to 1
 
META TOPICPARENT name="SupportBioLab"
Changed:
<
<
Medical Bioinformatics

Proteomics analysis
>
>
Medical Bioinformatics

Back to menu

Proteomics analysis
 

Under construction \ No newline at end of file
Revision 2
18 Dec 2009 - Main.AngelaLuijf
Line: 1 to 1
Changed:
<
<
META TOPICPARENT name="MicroarrayBioLab"
>
>
META TOPICPARENT name="SupportBioLab"
 
Medical Bioinformatics

Proteomics analysis

Under construction
 
This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Foswiki? Send feedback