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PrePostStudy
(20 Jan 2005,
JoanZhang
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---++ Pre&Post Treatment Study * Start Date: 16 Nov 2004 * Research Drive Directory: /Taguchi/041112/ * Data Type: <nop>MassSpec * Notes: 4 spectra of same patient in K2099 and K2199 were collected on 4 different dates. * Status: * old normalized data set * graph : 100% * QC : 100% * new normalized data set * graph : 100% * QC : 100% * Leave One Out : failed (data did not pass QC) ---++++ Output * old normalization * intensity graph: .\old normalization\graph * QC: .\old normalization\QC\result * QC summary: .\old normalization\QC * new normalization * intensity graph: .\new normalization\graph * cluster results: .\new normalization\cluster * QC: .\new normalization\QC\result * QC summary: .\new normalization * an detailed example of intensity/cluster : .\example.ppt ---++++ Data Sets Background ---++++ ==data sets with old normalization method== * data come from two hospitals: Kanazawa and JFCR. * data from Kanazawa have laser intensity 2099 and 2199, JFCR have laser intensity 2399. * "baseline" data are samples before taking Iressa, "day14" data are samples after taking Iressa 14 days. * all data sets have done smoothing, baseline correction, and calibration by investigator, then binned and normalized by Huiming. Data haven't taken log transformation. * each patient have 3 samples except patient31 in JFCR_BaseLine_2399. * all samples are collected on same day, but spectra are collected on different day. Kanazawa2199 is collected a few months before Kanazawa 2099. * Kanazawa2199 includes both pre and post samples. * data set and patient info * data set 1 = Kanazawa2099 pre: 26 (3 spectra per patient, all 3 spectra are collected in 3 different days) * data set 2 = Kanazawa2099 post: 17 (3 spectra per patient,all 3 spectra are collected in 3 different days) * data set 3 = JFCR2399 pre : 43 (3 spectra per patient except patient 31 only have 2 spectra) * data set 4 = JFCR2399 post: 35 (3 spectra per patient) * data set 5 = Kanazawa2199 : pre - 26 (1 spectrum per patient collected different day with K2099), post - 17 (1 spectrum per patient,collected different day with K2099) ---++++ ==data sets with new normalization method== * same background as old data sets except using different way to normaliz ---++++ Analysis Requests * ==old normalization== * graph of expression(sort by peaks and spectra) * each data set alone * 1 vs. 2 * 1 vs. 3 * 1 vs. 5 pre part * 2 vs. 4 * 2 vs. 5 post part * 3 vs. 4 * 1 and 5 pre part (include cluster to show day to day variance) * 2 and 5 post part (include cluster to show day to day variance) * 1 (cluster to show day to day variance) * 2 (cluster to show day to day variance) * K2099 and K2199 pre: day to day (sort by date) * k2099 and k2199 post: day to day (sort by date) * K2099 and K2199 pre: by laser power * k2099 and k2199 post: by laser power * K2099(avg) and K2199 pre: by laser power * k2099(avg) and k2199 post: by laser power * k2099(avg) and JFCR(avg) pre: by hospital * k2099(avg) and JFCR(avg) post: by hospital * clustering * d1: K2099 pre and K2199 pre (total 26 patients) * d2: K2099 post and K2199 post (total 17 patients) * d3: JFCR pre (total 43 patients) * d4: JFCR post (total 35 patients) * d5: K2099 pre * d6: K2099 post * pre : average of K2099 vs. K2199 (Kappa agreement) * post : average of K2099 vs. K2199 (Kappa agreement) * QC analysis on all 5 data sets - method: use pre vs. pre, post vs. post * ==new normalization== * intensity expression * each data set alone * pre & post: K2099 vs. K2199 sort by date * pre & post: K2099 vs. K2199 sort by laser power * pre & post: K2099(avg) vs. K2199 sort by date * pre & post: K2099(avg) vs. K2199 sort by laser power * pre & post: K2099(avg) vs. JFCR(avg) sort by hospital * clustering * pre & post: K2099 * pre & post: K2099 vs. K2199 * pre & post: K2099(avg) vs. K2199 * pre & post: JFCR * QC analysis on all data set plus pre/post K2099 vs. K2199 * ==Correlation== : K2099 pre, K2099 post, JFCR pre, JFCR post, K2099&K2199 pre, K2099&K2199 post * ==ICC== : K2099 pre, K2099 post, JFCR pre, JFCR post, K2099&K2199 pre, K2099&K2199 post * ==Kappa Agreement== :K2099 pre, K2099 post, JFCR pre, JFCR post, K2099&K2199 pre, K2099&K2199 post * ==Leave One Out== * generate the 3rd data set form data set 1&2 (as testing set), data set 3&5(as training set) : value = (post - pre)/pre * run paired TTest if both pre and post have intensity (proc means) ---++++ Change Log: ---++++ Contact Info: * Primary Study Contact Person: Fumiko Taguchi (6-3819) ---++++ Analysts * Main.NimishGautam * Main.JoanZhang
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Topic revision: r19 - 20 Jan 2005,
JoanZhang
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