opensesame() behind the scene
altuda opened this issue · comments
Hello, I would like to kindly ask you why there is a difference in betas between the opensesame and the supposedly equivalent function. Were there some changes inside the opensesame()?
betas=do.call(cbind,mclapply(searchIDATprefixes(idat_dir), function(px) getBetas(dyeBiasNL(noob(pOOBAH(readIDATpair(px))))), mc.cores=2))
head(betas)
4207113116_A 4207113116_B
cg00000292 0.89670032 0.21734243
cg00002426 0.02775268 0.96295625
cg00003994 0.03310098 0.05221246
cg00005847 0.45003310 0.37307742
cg00006414 0.08853971 0.13978757
cg00007981 0.02775176 0.02527006
betas2 = openSesame(idat_dir)
head(betas2)
4207113116_A 4207113116_B
cg00000292 0.89382957 0.21242243
cg00002426 0.02624318 0.96299515
cg00003994 0.03059269 0.05339756
cg00005847 0.44972050 0.37410379
cg00006414 0.09228522 0.13570582
cg00007981 0.02626539 0.02593596
all(betas == betas2, na.rm=T)
[1] FALSE
Hi the slight difference might come from qualityMask. See more details at openSesame's prep= argument.
https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/sesame.html#Data_Preprocessing
and here
https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/sesame.html#Preprocessing_Function_Code
Hello,
Thank you for your response.