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= Regression analysis of UCLA SZ data (additional different age cutoff of grouping of data on LDA) = * Suggestions from lab meeting on 2012.05.16 ** LDA: randomly choose samples for training and (have UCLA-SZ and UCSD-GA on training and testing data sets) ** LDA: Change age cutoff from 40 to different number (50, 60 or 70) and see how accurate the samples can be classified at different age cutoff. **PCA: I also performed PCA and changed the color of each sample in scatter plot based on the age cutoff. * Training and testing data set ** list 1-96 =>UCSD-SZ, 97-169 => UCSD-GA ** trainAge <- c(1:40, 91:132) ** testAge <- c(41:90, 133:169) == Regression analysis on age : LDA and PCA == '''Scripts''': (Note: used the same template, but change color code based on age cutoff and labeling) '''LDA''': [[Media:lda_age-40_10FDR.txt| lda_age-40_10FDR.txt]] '''PCA''': [[Media:plot_pca_age-40_10FDR.txt| plot_pca_age-40_10FDR.txt]], [[Media:plot_pca_age-40_label-age_10FDR.txt| plot_pca_age-40_label-age_10FDR.txt]] '''Color code''': [[Media:color.code_age_cutoff-40-70.txt| color.code_age_cutoff-40-70.txt]] '''PC scores (PC1-3) and labeling''': [[Media:Age-40_PCscores_Labeling.txt| Age-40_PCscores_Labeling.txt]], [[Media:Age-50_PCscores_Labeling.txt| Age-50_PCscores_Labeling.txt]], [[Media:Age-60_PCscores_Labeling.txt| Age-60_PCscores_Labeling.txt]], [[Media:Age-70_PCscores_Labeling.txt| Age-70_PCscores_Labeling.txt]] '''Tables of raw data'''<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Age cutoff 40 (10% FDR)''' | align="center" style="background:#f0f0f0;"|'''Predicted\Truth''' | align="center" style="background:#f0f0f0;"|'''Adult''' | align="center" style="background:#f0f0f0;"|'''Young adult''' | align="center" style="background:#f0f0f0;"|'''Correct''' | align="center" style="background:#f0f0f0;"|'''FALSE''' | align="center" style="background:#f0f0f0;"|'''Total''' |- | Training||Adult ||54||2||77||5||82 |- | ||Young adult||3||23|||||| |- | |||||||||||| |- | Testing||Adult ||59||1||85||2||87 |- | ||Young adult||1||26|||||| |- | |||||||||||| |- | Cross validation||Adult ||112||3||161||8||169 |- | ||Young adult||5||49|||||| |}<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Age cutoff 50 (10% FDR)''' | align="center" style="background:#f0f0f0;"|'''Predicted\Truth''' | align="center" style="background:#f0f0f0;"|'''Adult''' | align="center" style="background:#f0f0f0;"|'''Young adult''' | align="center" style="background:#f0f0f0;"|'''Correct''' | align="center" style="background:#f0f0f0;"|'''FALSE''' | align="center" style="background:#f0f0f0;"|'''Total''' |- | Training||Adult ||51||4||76||6||82 |- | ||Young adult||2||25|||||| |- | |||||||||||| |- | Testing||Adult ||58||0||85||2||87 |- | ||Young adult||2||27|||||| |- | |||||||||||| |- | Cross validation||Adult ||110||4||162||7||169 |- | ||Young adult||3||52|||||| |}<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Age cutoff 60 (10% FDR)''' | align="center" style="background:#f0f0f0;"|'''Predicted\Truth''' | align="center" style="background:#f0f0f0;"|'''Adult''' | align="center" style="background:#f0f0f0;"|'''Young adult''' | align="center" style="background:#f0f0f0;"|'''Correct''' | align="center" style="background:#f0f0f0;"|'''FALSE''' | align="center" style="background:#f0f0f0;"|'''Total''' |- | Training||Adult ||32||7||72||10||82 |- | ||Young adult||3||40|||||| |- | |||||||||||| |- | Testing||Adult ||40||13||71||16||87 |- | ||Young adult||3||31|||||| |- | |||||||||||| |- | Cross validation||Adult ||72||22||141||28||169 |}<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Age cutoff 70 (10% FDR)''' | align="center" style="background:#f0f0f0;"|'''Predicted\Truth''' | align="center" style="background:#f0f0f0;"|'''Adult''' | align="center" style="background:#f0f0f0;"|'''Young adult''' | align="center" style="background:#f0f0f0;"|'''Correct''' | align="center" style="background:#f0f0f0;"|'''FALSE''' | align="center" style="background:#f0f0f0;"|'''Total''' |- | Training||Adult ||14||4||70||12||82 |- | ||Young adult||8||56|||||| |- | |||||||||||| |- | Testing||Adult ||16||8||68||19||87 |- | ||Young adult||11||52|||||| |- | |||||||||||| |- | Cross validation||Adult ||30||12||138||31||169 |- | ||Young adult||19||108|||||| |}<br> ''' Table of accuracy and misclassification rate ''' {| {{table}} border =1 | align="center" style="background:#f0f0f0;"|'''Age cutoff''' | align="center" style="background:#f0f0f0;"|'''Training (Accuracy of allocation)''' | align="center" style="background:#f0f0f0;"|'''Misclassicication rate''' | align="center" style="background:#f0f0f0;"|'''Testing (quality of model)''' | align="center" style="background:#f0f0f0;"|'''Misclassicication rate''' | align="center" style="background:#f0f0f0;"|'''Cross validation''' | align="center" style="background:#f0f0f0;"|'''Misclassicication rate''' |- | 40||77 of 82||6.10%||85 of 87||2.30%||161 of 169||4.73% |- | 50||76 of 82||7.32%||85 of 87||2.30%||162 of 169||4.14% |- | 60||72 of 82||12.20%||71 of 87||18.39%||141 of 169||16.57% |- | 70||70 of 82||14.63%||68 of 87||21.84%||138 of 169||18.34% |}<br> == PCA plots == Note: For the PCA plot labeled with age numbers. The number after dot(.) like 22.1 or 22.2 represent the duplication of sampleIDs with the same age. ''' Age cutoff: 40 ''' [[File:UCLA-GA_age-cutoff40_10FDR_pcaplot1.png| 580px]] [[File:UCLA-GA_age-cutoff40_10FDR_pcaplot2.png| 580px]] '''Additional plots:''' [[Media:UCLA-GA_age-cutoff40_10FDR_pca-label-age_plot1.pdf| UCLA-GA_age-cutoff40_10FDR_pca-label-age_plot1]] [[Media:UCLA-GA_age-cutoff40_10FDR_pca-label-age_plot2.pdf| UCLA-GA_age-cutoff40_10FDR_pca-label-age_plot2]] [[Media:UCLA-GA_age-cutoff40_10FDR_pcaplot1.pdf| UCLA-GA_age-cutoff40_10FDR_pcaplot1]] [[Media:UCLA-GA_age-cutoff40_10FDR_pcaplot2.pdf| UCLA-GA_age-cutoff40_10FDR_pcaplot2]] ''' Age cutoff: 50 ''' [[File:UCLA-GA_age-cutoff50_10FDR_pcaplot1.png| 580px]] [[File:UCLA-GA_age-cutoff50_10FDR_pcaplot2.png| 580px]] '''Additional plots:''' [[Media:UCLA-GA_age-cutoff50_10FDR_pca-label-age_plot1.pdf| UCLA-GA_age-cutoff50_10FDR_pca-label-age_plot1]] [[Media:UCLA-GA_age-cutoff50_10FDR_pca-label-age_plot2.pdf| UCLA-GA_age-cutoff50_10FDR_pca-label-age_plot2]] [[Media:UCLA-GA_age-cutoff50_10FDR_pcaplot1.pdf| UCLA-GA_age-cutoff50_10FDR_pcaplot1]] [[Media:UCLA-GA_age-cutoff50_10FDR_pcaplot2.pdf| UCLA-GA_age-cutoff50_10FDR_pcaplot2]] ''' Age cutoff: 60 ''' [[File:UCLA-GA_age-cutoff60_10FDR_pcaplot1.png| 580px]] [[File:UCLA-GA_age-cutoff60_10FDR_pcaplot2.png| 580px]] '''Additional plots:''' [[Media:UCLA-GA_age-cutoff60_10FDR_pca-label-age_plot1.pdf| UCLA-GA_age-cutoff60_10FDR_pca-label-age_plot1]] [[Media:UCLA-GA_age-cutoff60_10FDR_pca-label-age_plot2.pdf| UCLA-GA_age-cutoff60_10FDR_pca-label-age_plot2]] [[Media:UCLA-GA_age-cutoff60_10FDR_pcaplot1.pdf| UCLA-GA_age-cutoff60_10FDR_pcaplot1]] [[Media:UCLA-GA_age-cutoff60_10FDR_pcaplot2.pdf| UCLA-GA_age-cutoff60_10FDR_pcaplot2]] ''' Age cutoff: 70 ''' [[File:UCLA-GA_age-cutoff70_10FDR_pcaplot1.png| 580px]] [[File:UCLA-GA_age-cutoff70_10FDR_pcaplot2.png| 580px]] '''Additional plots:''' [[Media:UCLA-GA_age-cutoff70_10FDR_pca-label-age_plot1.pdf| UCLA-GA_age-cutoff70_10FDR_pca-label-age_plot1]] [[Media:UCLA-GA_age-cutoff70_10FDR_pca-label-age_plot2.pdf| UCLA-GA_age-cutoff70_10FDR_pca-label-age_plot2]] [[Media:UCLA-GA_age-cutoff70_10FDR_pcaplot1.pdf| UCLA-GA_age-cutoff70_10FDR_pcaplot1]] [[Media:UCLA-GA_age-cutoff70_10FDR_pcaplot2.pdf| UCLA-GA_age-cutoff70_10FDR_pcaplot2]] '''The distribution and fraction of UCLA-SZ and UCSD-GA' AGE''' A<-read.table("UCLA-SZ_UCSD-GA.age.txt", sep=",") age<-as.numeric(A) length(age) ageFact<-factor(age) levels(ageFact) summary(ageFact) summary(ageFact) '''Age''' 19 21 22 23 24 25 26 27 28 29 30 31 32 33 35 36 37 39 40 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 '''number''' 1 3 3 4 4 2 3 6 5 2 4 3 2 1 4 2 1 1 1 2 2 2 3 4 3 6 3 4 5 2 3 1 4 3 2 4 5 2 2 4 '''Age''' 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 '''number''' 2 5 2 3 3 1 2 3 2 3 5 7 5 2 3 1 2 '''Summary'''<br> * Continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-14
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