Kun:LabNotes/CpgSeq/2011-10-14: Difference between revisions

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m (Created page with '==Analysis of BSPP data from Geographic Astrophy (GA) patients== *96 blood samples from cases and controls were provided by Kang Zhang's group. *Noi performed the BSPP capture an…')
 
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===Regression analysis===
===Regression analysis===
*The working directory is on genome-miner
  /home/kunzhang/mQTL/KangZhang_GA
*One data set (2200001) was removed due to low capture efficiency and low sequencing depth.
*One data set (2200001) was removed due to low capture efficiency and low sequencing depth.
*Methylation levels from the rest of 95 samples were combined into a matrix (up to 20% missing values was allowed):
*Methylation levels from the rest of 95 samples were combined into a matrix (up to 20% missing values was allowed):

Revision as of 01:27, 15 October 2011

Analysis of BSPP data from Geographic Astrophy (GA) patients

  • 96 blood samples from cases and controls were provided by Kang Zhang's group.
  • Noi performed the BSPP capture and the sequencing was done in BioGem (110929_SN1001)

Summary statistics on sequencing, mapping and CpG methylation calling

Noi should fill in this part.

Regression analysis

  • The working directory is on genome-miner
  /home/kunzhang/mQTL/KangZhang_GA
  • One data set (2200001) was removed due to low capture efficiency and low sequencing depth.
  • Methylation levels from the rest of 95 samples were combined into a matrix (up to 20% missing values was allowed):
  allBED2Matrix.pl BED 76 1 0.1 > KangZhang_GA_BSPP_95_methylationMatrix.txt &
  • I ended up getting a matrix containing 136,417 variable CpG sites.
  • I wrote a Perl Script to perform linear regression on five factors: disease status, sex, age, BMI, smoking: GA_methylation_regression.txt.
  • Sites that might be significantly contributed by one of these factors were reported.
    • I used a stringent cutoff of 3.5 for the t-statistics on reporting the data in individual files (allowed for more detailed analysis in R).
    • The test statistics for all the tested sites were also reported in a separate file.