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WfccmQcAgreement
(09 May 2005,
JoanZhang
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---+++ Kappa Value and Agreement Rate algorithms * 1. For each gene/feature, convert their are values to binary</br> * new value(proteinomic data) = 1 </br>if old value is greater than 1, </br>else new value = 0 * new value(Microarray data) = 1 </br>if old value is not a null, </br>else new value = null * 2. N = total number of genes/features * 3. YY = values of both samples are 1s</br> NN = values of both samples are 0s/missing</br> YN = value of sample1 is 1, and value of sample2 is 0/missing</br> NY = value of sample1 is 0, and value of sample2 is 0/missing * 4. Pct_YY = YY / N </br> Pct_NN = NN / N </br> Pct_YN = YN / N </br>Pct_NY = NY / N * 5. ==Agreement rate of sample1 and sampe2== = Pct_YY + Pct_NN * 6. Kappa Value of Sample1 and sample2</br> Observed agreement = Pct_YY + Pct_NN </br> Chance Agreement = (Pct_NN + Pct_NY)*(Pct_NN + Pct_YN) + (Pct_NY + Pct_YY)*(Pct_YN + Pct_YY)</br> ==Kappa Value== = (Observed agreement - Chance Agreement)/(1 - Chance Agreement ) [[%ATTACHURL%/example2.xls][Real Example]]
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Topic revision: r5 - 09 May 2005,
JoanZhang
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