Pre&Post Treatment Study

  • Start Date: 16 Nov 2004
  • Research Drive Directory: /Taguchi/041112/
  • Data Type: 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

This topic: Main > Projects > MicroArrayMassSpec > PrePostStudy
Topic revision: 20 Jan 2005, JoanZhang
 
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