Supervised analysis of MS images using Cardinal
نویسنده
چکیده
2 Analysis of a renal cell carcinoma (RCC) cancer dataset 1 2.1 Pre-processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.1.1 Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.1.2 Resampling to unit resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.1.3 Subsetting the dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.2 Visualizing the dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2.1 Visualization of molecular ion images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2.2 Exploratory analysis using PCA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.3 Classification using PLS-DA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 2.3.1 Cross-validation with partial least squares . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.3.2 Plotting the classified images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.3.3 Plotting and interpretting the coefficients of the m/z values . . . . . . . . . . . . . . . . . . 8 2.4 Classification using O-PLS-DA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 2.4.1 Cross-validation with partial least squares . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 2.4.2 Plotting the classified images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 2.4.3 Plotting and interpretting the coefficients of the m/z values . . . . . . . . . . . . . . . . . . 10 2.5 Classification using spatial shrunken centroids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.5.1 Cross-validation with spatial shrunken centroids . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.5.2 Plotting the classified images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.5.3 Plotting and interpreting the t-statistics of the m/z values . . . . . . . . . . . . . . . . . . . 14
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