removeBatchEffect problem
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@john-coulthard-3077
Last seen 9.6 years ago
Hi I'm having troubles with the removeBatchEffect function. It seems that whatever I put in as the 'design' I get the same result out of removeBatchEffect(); Perhaps I'm not using the right syntax for the 'design'? Below is each line of the function run individually and the output from the line using 'design' with various inputs; Always the same output?! My design is 4x2x2; 4 tissues(T) x 2 subgroups(S) x 2 days(D) and the col order in e.qn is... T1S1D1, T1S2D1, T1S1D2, T1S2D2, T2S1D1, T2S2D1, T2S1D2, T2S2D2, T3S1D1, T3S2D1, T3S1D2, T3S2D2, T4S1D1, T4S2D1, T4S1D2, T4S2D2, And it's the day(D) effect I'm trying to remove. Can anyone point me to the right way to run this. Many thanks John the command I started with... e.qn_batch_removed<-removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1 ,1,2,2),design=matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)) then line by line... > removeBatchEffect function (x, batch, design = matrix(1, ncol(x), 1)) { x <- as.matrix(x) batch <- as.factor(batch) contrasts(batch) <- contr.sum(levels(batch)) X <- model.matrix(~batch)[, -1, drop = FALSE] X <- qr.resid(qr(design), X) qrX <- qr(X) t(qr.resid(qrX, t(x))) } <environment: namespace:limma=""> > > x <- as.matrix(e.qn) > batch <- as.factor(c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2)) > contrasts(batch) <- contr.sum(levels(batch)) > X <- model.matrix(~batch)[, -1, drop = FALSE] > qr.resid(qr(matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)), X) batch1 1 1 2 1 3 -1 4 -1 5 1 6 1 7 -1 8 -1 9 1 10 1 11 -1 12 -1 13 1 14 1 15 -1 16 -1 > qr.resid(qr(matrix(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2),16,1)), X) batch1 1 1 2 1 3 -1 4 -1 5 1 6 1 7 -1 8 -1 9 1 10 1 11 -1 12 -1 13 1 14 1 15 -1 16 -1 > qr.resid(qr(matrix(1,16,1)), X) batch1 1 1 2 1 3 -1 4 -1 5 1 6 1 7 -1 8 -1 9 1 10 1 11 -1 12 -1 13 1 14 1 15 -1 16 -1 > [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 12 hours ago
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Hi John, On 10/20/2011 6:42 AM, John Coulthard wrote: > Hi > > I'm having troubles with the removeBatchEffect function. It seems that whatever I put in as the 'design' I get the same result out of removeBatchEffect(); Perhaps I'm not using the right syntax for the 'design'? > > Below is each line of the function run individually and the output from the line using 'design' with various inputs; Always the same output?! > > My design is 4x2x2; 4 tissues(T) x 2 subgroups(S) x 2 days(D) and the col order in e.qn is... > T1S1D1, T1S2D1, T1S1D2, T1S2D2, T2S1D1, T2S2D1, T2S1D2, T2S2D2, T3S1D1, T3S2D1, T3S1D2, T3S2D2, T4S1D1, T4S2D1, T4S1D2, T4S2D2, > > And it's the day(D) effect I'm trying to remove. > > > Can anyone point me to the right way to run this. > > Many thanks > John > > the command I started with... > e.qn_batch_removed<-removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2 ,1,1,2,2),design=matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)) That isn't the correct design matrix. What you most likely want is design <- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) Best, Jim > then line by line... >> removeBatchEffect > function (x, batch, design = matrix(1, ncol(x), 1)) > { > x<- as.matrix(x) > batch<- as.factor(batch) > contrasts(batch)<- contr.sum(levels(batch)) > X<- model.matrix(~batch)[, -1, drop = FALSE] > X<- qr.resid(qr(design), X) > qrX<- qr(X) > t(qr.resid(qrX, t(x))) > } > <environment: namespace:limma=""> > > >> x<- as.matrix(e.qn) >> batch<- as.factor(c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2)) >> contrasts(batch)<- contr.sum(levels(batch)) >> X<- model.matrix(~batch)[, -1, drop = FALSE] >> qr.resid(qr(matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)), X) > batch1 > 1 1 > 2 1 > 3 -1 > 4 -1 > 5 1 > 6 1 > 7 -1 > 8 -1 > 9 1 > 10 1 > 11 -1 > 12 -1 > 13 1 > 14 1 > 15 -1 > 16 -1 >> qr.resid(qr(matrix(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2),16,1)), X) > batch1 > 1 1 > 2 1 > 3 -1 > 4 -1 > 5 1 > 6 1 > 7 -1 > 8 -1 > 9 1 > 10 1 > 11 -1 > 12 -1 > 13 1 > 14 1 > 15 -1 > 16 -1 >> qr.resid(qr(matrix(1,16,1)), X) > batch1 > 1 1 > 2 1 > 3 -1 > 4 -1 > 5 1 > 6 1 > 7 -1 > 8 -1 > 9 1 > 10 1 > 11 -1 > 12 -1 > 13 1 > 14 1 > 15 -1 > 16 -1 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Thanks Jim, but still regardless of the design matrix I give it the output is the same?! I must be missing something else. > design <- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) > head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),desig n=design)[,1:6]) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2))[,1:6]) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > design <- model.matrix(~factor(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2) )) > head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),desig n=design)[,1:6]) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > > Date: Thu, 20 Oct 2011 09:33:01 -0400 > From: jmacdon@med.umich.edu > To: bahhab@hotmail.com > CC: bioconductor@r-project.org > Subject: Re: [BioC] removeBatchEffect problem > > Hi John, > > On 10/20/2011 6:42 AM, John Coulthard wrote: > > Hi > > > > I'm having troubles with the removeBatchEffect function. It seems that whatever I put in as the 'design' I get the same result out of removeBatchEffect(); Perhaps I'm not using the right syntax for the 'design'? > > > > Below is each line of the function run individually and the output from the line using 'design' with various inputs; Always the same output?! > > > > My design is 4x2x2; 4 tissues(T) x 2 subgroups(S) x 2 days(D) and the col order in e.qn is... > > T1S1D1, T1S2D1, T1S1D2, T1S2D2, T2S1D1, T2S2D1, T2S1D2, T2S2D2, T3S1D1, T3S2D1, T3S1D2, T3S2D2, T4S1D1, T4S2D1, T4S1D2, T4S2D2, > > > > And it's the day(D) effect I'm trying to remove. > > > > > > Can anyone point me to the right way to run this. > > > > Many thanks > > John > > > > the command I started with... > > e.qn_batch_removed<-removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2 ,2,1,1,2,2),design=matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)) > > That isn't the correct design matrix. What you most likely want is > > design <- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) > > Best, > > Jim > > > > then line by line... > >> removeBatchEffect > > function (x, batch, design = matrix(1, ncol(x), 1)) > > { > > x<- as.matrix(x) > > batch<- as.factor(batch) > > contrasts(batch)<- contr.sum(levels(batch)) > > X<- model.matrix(~batch)[, -1, drop = FALSE] > > X<- qr.resid(qr(design), X) > > qrX<- qr(X) > > t(qr.resid(qrX, t(x))) > > } > > <environment: namespace:limma=""> > > > > > >> x<- as.matrix(e.qn) > >> batch<- as.factor(c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2)) > >> contrasts(batch)<- contr.sum(levels(batch)) > >> X<- model.matrix(~batch)[, -1, drop = FALSE] > >> qr.resid(qr(matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)), X) > > batch1 > > 1 1 > > 2 1 > > 3 -1 > > 4 -1 > > 5 1 > > 6 1 > > 7 -1 > > 8 -1 > > 9 1 > > 10 1 > > 11 -1 > > 12 -1 > > 13 1 > > 14 1 > > 15 -1 > > 16 -1 > >> qr.resid(qr(matrix(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2),16,1)), X) > > batch1 > > 1 1 > > 2 1 > > 3 -1 > > 4 -1 > > 5 1 > > 6 1 > > 7 -1 > > 8 -1 > > 9 1 > > 10 1 > > 11 -1 > > 12 -1 > > 13 1 > > 14 1 > > 15 -1 > > 16 -1 > >> qr.resid(qr(matrix(1,16,1)), X) > > batch1 > > 1 1 > > 2 1 > > 3 -1 > > 4 -1 > > 5 1 > > 6 1 > > 7 -1 > > 8 -1 > > 9 1 > > 10 1 > > 11 -1 > > 12 -1 > > 13 1 > > 14 1 > > 15 -1 > > 16 -1 > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > [[alternative HTML version deleted]]
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Hi John, I don't know what to tell you. > x [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > design <- model.matrix(~factor(c(1,2,1,2,3,4))) > removeBatchEffect(x, rep(c(1,2,1), each=2), design=design) [,1] [,2] [,3] [,4] [,5] [,6] [1,] 20.59406 17.68205 22.04684 16.22926 23.16786 20.83750 [2,] 26.99328 23.48398 27.42751 23.04976 24.70404 22.56948 [3,] 26.87191 23.95813 26.85852 23.97153 22.84880 23.33938 [4,] 21.42821 21.10935 21.36638 21.17117 20.31454 20.50233 [5,] 32.36628 30.12798 32.00640 30.48785 31.11213 30.74922 [6,] 22.38064 21.90990 22.31125 21.97928 20.94986 21.76465 Works for me with the small subset of data you supply. Best, Jim On 10/20/2011 11:02 AM, John Coulthard wrote: > Thanks Jim, but still regardless of the design matrix I give it the output is the same?! I must be missing something else. > >> design<- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) >> head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),desi gn=design)[,1:6]) > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 >> head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2))[,1:6]) > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 >> design<- model.matrix(~factor(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2) )) >> head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),desi gn=design)[,1:6]) > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > > > >> Date: Thu, 20 Oct 2011 09:33:01 -0400 >> From: jmacdon at med.umich.edu >> To: bahhab at hotmail.com >> CC: bioconductor at r-project.org >> Subject: Re: [BioC] removeBatchEffect problem >> >> Hi John, >> >> On 10/20/2011 6:42 AM, John Coulthard wrote: >>> Hi >>> >>> I'm having troubles with the removeBatchEffect function. It seems that whatever I put in as the 'design' I get the same result out of removeBatchEffect(); Perhaps I'm not using the right syntax for the 'design'? >>> >>> Below is each line of the function run individually and the output from the line using 'design' with various inputs; Always the same output?! >>> >>> My design is 4x2x2; 4 tissues(T) x 2 subgroups(S) x 2 days(D) and the col order in e.qn is... >>> T1S1D1, T1S2D1, T1S1D2, T1S2D2, T2S1D1, T2S2D1, T2S1D2, T2S2D2, T3S1D1, T3S2D1, T3S1D2, T3S2D2, T4S1D1, T4S2D1, T4S1D2, T4S2D2, >>> >>> And it's the day(D) effect I'm trying to remove. >>> >>> >>> Can anyone point me to the right way to run this. >>> >>> Many thanks >>> John >>> >>> the command I started with... >>> e.qn_batch_removed<-removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2 ,2,1,1,2,2),design=matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)) >> That isn't the correct design matrix. What you most likely want is >> >> design<- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) >> >> Best, >> >> Jim >> >> >>> then line by line... >>>> removeBatchEffect >>> function (x, batch, design = matrix(1, ncol(x), 1)) >>> { >>> x<- as.matrix(x) >>> batch<- as.factor(batch) >>> contrasts(batch)<- contr.sum(levels(batch)) >>> X<- model.matrix(~batch)[, -1, drop = FALSE] >>> X<- qr.resid(qr(design), X) >>> qrX<- qr(X) >>> t(qr.resid(qrX, t(x))) >>> } >>> <environment: namespace:limma=""> >>> >>> >>>> x<- as.matrix(e.qn) >>>> batch<- as.factor(c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2)) >>>> contrasts(batch)<- contr.sum(levels(batch)) >>>> X<- model.matrix(~batch)[, -1, drop = FALSE] >>>> qr.resid(qr(matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)), X) >>> batch1 >>> 1 1 >>> 2 1 >>> 3 -1 >>> 4 -1 >>> 5 1 >>> 6 1 >>> 7 -1 >>> 8 -1 >>> 9 1 >>> 10 1 >>> 11 -1 >>> 12 -1 >>> 13 1 >>> 14 1 >>> 15 -1 >>> 16 -1 >>>> qr.resid(qr(matrix(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2),16,1)), X) >>> batch1 >>> 1 1 >>> 2 1 >>> 3 -1 >>> 4 -1 >>> 5 1 >>> 6 1 >>> 7 -1 >>> 8 -1 >>> 9 1 >>> 10 1 >>> 11 -1 >>> 12 -1 >>> 13 1 >>> 14 1 >>> 15 -1 >>> 16 -1 >>>> qr.resid(qr(matrix(1,16,1)), X) >>> batch1 >>> 1 1 >>> 2 1 >>> 3 -1 >>> 4 -1 >>> 5 1 >>> 6 1 >>> 7 -1 >>> 8 -1 >>> 9 1 >>> 10 1 >>> 11 -1 >>> 12 -1 >>> 13 1 >>> 14 1 >>> 15 -1 >>> 16 -1 >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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> Date: Thu, 20 Oct 2011 11:32:30 -0400 > From: jmacdon@med.umich.edu > To: bahhab@hotmail.com > CC: bioconductor@r-project.org > Subject: Re: [BioC] removeBatchEffect problem > > Hi John, > > I don't know what to tell you. > > > x > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > > > design <- model.matrix(~factor(c(1,2,1,2,3,4))) > > removeBatchEffect(x, rep(c(1,2,1), each=2), design=design) > [,1] [,2] [,3] [,4] [,5] [,6] > [1,] 20.59406 17.68205 22.04684 16.22926 23.16786 20.83750 > [2,] 26.99328 23.48398 27.42751 23.04976 24.70404 22.56948 > [3,] 26.87191 23.95813 26.85852 23.97153 22.84880 23.33938 > [4,] 21.42821 21.10935 21.36638 21.17117 20.31454 20.50233 > [5,] 32.36628 30.12798 32.00640 30.48785 31.11213 30.74922 > [6,] 22.38064 21.90990 22.31125 21.97928 20.94986 21.76465 > > Works for me with the small subset of data you supply. Thanks Jim, My issue was that if I then ran removeBatchEffect with a different design element (just to prove to myself I was doing this right) I got the same results; i.e. the design element appeared to be having no effect. But that didn't happen with just six cols of data (following on from what you have above)... > design <- model.matrix(~factor(c(1,1,1,2,2,2))) > removeBatchEffect(x, rep(c(1,2,1), each=2), design=design) V1 V2 V3 V4 V5 V6 [1,] 20.49073 17.57872 23.00172 17.18414 22.31631 19.98595 [2,] 27.26734 23.75804 26.89355 22.51580 24.96394 22.82938 [3,] 27.33608 24.42230 26.08487 23.19789 23.15828 23.64886 [4,] 21.71513 21.39627 21.07960 20.88439 20.31440 20.50219 [5,] 32.52130 30.28300 31.90092 30.38237 31.06259 30.69968 [6,] 22.58024 22.10950 22.04858 21.71661 21.01292 21.82771 so I tried again with 16 columns and there are differences between design <- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8))) and design<- model.matrix(~factor(c(1,1,1,1,2,2,2,2,1,1,1,1,2,2,2,2) )) it's just they are so small they get lost in the rounding. So I guess it is working as it should but my method of convincing myself that it works was seriously flawed. Thanks for your time. > x<-head(e.qn) #the first 6 rows of my data; see below > design<- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) > y<-removeBatchEffect(x, rep(c(1,1,2,2), 4), design=design) > design<- model.matrix(~factor(c(1,1,1,1,2,2,2,2,1,1,1,1,2,2,2,2) )) > z<-removeBatchEffect(x, rep(c(1,1,2,2), 4), design=design) > max(y-z) [1] 7.105427e-15 > format(z[1,1], digits=20) [1] "21.342279433232679509" > format(y[1,1], digits=20) [1] "21.342279433232683061" > x [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.38993 18.47792 21.25097 15.43339 23.21551 20.88515 [2,] 27.19205 23.68276 27.22873 22.85098 24.88866 22.75410 [3,] 26.83332 23.91955 26.89710 24.01012 22.65553 23.14611 [4,] 21.46395 21.14509 21.33064 21.13543 20.06322 20.25101 [5,] 32.35783 30.11952 32.01486 30.49631 30.89911 30.53621 [6,] 21.98646 21.51572 22.70543 22.37346 20.41914 21.23393 [,7] [,8] [,9] [,10] [,11] [,12] [1,] 22.96322 19.39987 23.04609 20.16191 23.91040 20.03716 [2,] 24.79286 22.31044 27.18536 24.02368 27.96298 23.38279 [3,] 24.08869 24.10216 24.31715 23.68728 24.82202 24.48001 [4,] 20.86551 21.10980 20.98385 20.38379 22.12131 21.91251 [5,] 30.27100 31.07816 30.83535 30.68225 32.35783 30.89911 [6,] 21.75568 22.39880 21.24631 20.87767 22.90156 22.74874 [,13] [,14] [,15] [,16] [1,] 20.96133 19.92078 24.62166 19.67955 [2,] 27.51171 23.99884 26.76161 22.99287 [3,] 25.50943 24.19461 24.78192 24.17332 [4,] 21.55765 21.09746 21.33941 21.15254 [5,] 31.54015 29.93768 32.12096 31.07816 [6,] 21.13245 21.39392 21.68297 21.73048 > y [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 [,7] [,8] [,9] [,10] [,11] [,12] [1,] 23.01087 19.44752 22.99844 20.11426 23.95805 20.08481 [2,] 24.97748 22.49506 27.00074 23.83906 28.14760 23.56740 [3,] 23.89542 23.90888 24.51042 23.88055 24.62875 24.28674 [4,] 20.61419 20.85848 21.23517 20.63511 21.86999 21.66119 [5,] 30.05798 30.86514 31.04836 30.89527 32.14481 30.68609 [6,] 21.22496 21.86808 21.77704 21.40839 22.37084 22.21802 [,13] [,14] [,15] [,16] [1,] 20.91368 19.87313 24.66931 19.72720 [2,] 27.32709 23.81422 26.94623 23.17748 [3,] 25.70270 24.38789 24.58865 23.98005 [4,] 21.80897 21.34879 21.08809 20.90122 [5,] 31.75316 30.15070 31.90794 30.86514 [6,] 21.66317 21.92464 21.15225 21.19976 > z [,1] [,2] [,3] [,4] [,5] [,6] [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 [,7] [,8] [,9] [,10] [,11] [,12] [1,] 23.01087 19.44752 22.99844 20.11426 23.95805 20.08481 [2,] 24.97748 22.49506 27.00074 23.83906 28.14760 23.56740 [3,] 23.89542 23.90888 24.51042 23.88055 24.62875 24.28674 [4,] 20.61419 20.85848 21.23517 20.63511 21.86999 21.66119 [5,] 30.05798 30.86514 31.04836 30.89527 32.14481 30.68609 [6,] 21.22496 21.86808 21.77704 21.40839 22.37084 22.21802 [,13] [,14] [,15] [,16] [1,] 20.91368 19.87313 24.66931 19.72720 [2,] 27.32709 23.81422 26.94623 23.17748 [3,] 25.70270 24.38789 24.58865 23.98005 [4,] 21.80897 21.34879 21.08809 20.90122 [5,] 31.75316 30.15070 31.90794 30.86514 [6,] 21.66317 21.92464 21.15225 21.19976 > y-z [,1] [,2] [,3] [,4] [1,] 3.552714e-15 0.000000e+00 -3.552714e-15 -1.776357e-15 [2,] 3.552714e-15 0.000000e+00 0.000000e+00 0.000000e+00 [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [5,] -7.105427e-15 0.000000e+00 0.000000e+00 -7.105427e-15 [6,] 7.105427e-15 3.552714e-15 0.000000e+00 0.000000e+00 [,5] [,6] [,7] [,8] [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [3,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [5,] 0.000000e+00 0.000000e+00 -7.105427e-15 -7.105427e-15 [6,] 3.552714e-15 3.552714e-15 0.000000e+00 0.000000e+00 [,9] [,10] [,11] [,12] [1,] 3.552714e-15 3.552714e-15 0.000000e+00 -3.552714e-15 [2,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [3,] 0.000000e+00 0.000000e+00 0.000000e+00 -3.552714e-15 [4,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 [5,] 0.000000e+00 0.000000e+00 7.105427e-15 0.000000e+00 [6,] 0.000000e+00 3.552714e-15 0.000000e+00 0.000000e+00 [,13] [,14] [,15] [,16] [1,] 0.000000e+00 0 -3.552714e-15 -3.552714e-15 [2,] -3.552714e-15 0 0.000000e+00 0.000000e+00 [3,] -3.552714e-15 0 0.000000e+00 0.000000e+00 [4,] 0.000000e+00 0 0.000000e+00 0.000000e+00 [5,] 0.000000e+00 0 0.000000e+00 -7.105427e-15 [6,] 0.000000e+00 0 -3.552714e-15 -3.552714e-15 > > > Best, > > Jim > > > > On 10/20/2011 11:02 AM, John Coulthard wrote: > > Thanks Jim, but still regardless of the design matrix I give it the output is the same?! I must be missing something else. > > > >> design<- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) > >> head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),de sign=design)[,1:6]) > > [,1] [,2] [,3] [,4] [,5] [,6] > > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > >> head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2))[,1:6]) > > [,1] [,2] [,3] [,4] [,5] [,6] > > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > >> design<- model.matrix(~factor(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2) )) > >> head(removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2),de sign=design)[,1:6]) > > [,1] [,2] [,3] [,4] [,5] [,6] > > [1,] 21.34228 18.43027 21.29862 15.48104 23.16786 20.83750 > > [2,] 27.00744 23.49814 27.41335 23.03560 24.70404 22.56948 > > [3,] 27.02660 24.11282 26.70383 23.81685 22.84880 23.33938 > > [4,] 21.71527 21.39641 21.07932 20.88411 20.31454 20.50233 > > [5,] 32.57084 30.33254 31.80184 30.28329 31.11213 30.74922 > > [6,] 22.51718 22.04644 22.17471 21.84274 20.94986 21.76465 > > > > > > > >> Date: Thu, 20 Oct 2011 09:33:01 -0400 > >> From: jmacdon@med.umich.edu > >> To: bahhab@hotmail.com > >> CC: bioconductor@r-project.org > >> Subject: Re: [BioC] removeBatchEffect problem > >> > >> Hi John, > >> > >> On 10/20/2011 6:42 AM, John Coulthard wrote: > >>> Hi > >>> > >>> I'm having troubles with the removeBatchEffect function. It seems that whatever I put in as the 'design' I get the same result out of removeBatchEffect(); Perhaps I'm not using the right syntax for the 'design'? > >>> > >>> Below is each line of the function run individually and the output from the line using 'design' with various inputs; Always the same output?! > >>> > >>> My design is 4x2x2; 4 tissues(T) x 2 subgroups(S) x 2 days(D) and the col order in e.qn is... > >>> T1S1D1, T1S2D1, T1S1D2, T1S2D2, T2S1D1, T2S2D1, T2S1D2, T2S2D2, T3S1D1, T3S2D1, T3S1D2, T3S2D2, T4S1D1, T4S2D1, T4S1D2, T4S2D2, > >>> > >>> And it's the day(D) effect I'm trying to remove. > >>> > >>> > >>> Can anyone point me to the right way to run this. > >>> > >>> Many thanks > >>> John > >>> > >>> the command I started with... > >>> e.qn_batch_removed<-removeBatchEffect(e.qn,c(1,1,2,2,1,1,2,2,1,1 ,2,2,1,1,2,2),design=matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)) > >> That isn't the correct design matrix. What you most likely want is > >> > >> design<- model.matrix(~factor(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8) )) > >> > >> Best, > >> > >> Jim > >> > >> > >>> then line by line... > >>>> removeBatchEffect > >>> function (x, batch, design = matrix(1, ncol(x), 1)) > >>> { > >>> x<- as.matrix(x) > >>> batch<- as.factor(batch) > >>> contrasts(batch)<- contr.sum(levels(batch)) > >>> X<- model.matrix(~batch)[, -1, drop = FALSE] > >>> X<- qr.resid(qr(design), X) > >>> qrX<- qr(X) > >>> t(qr.resid(qrX, t(x))) > >>> } > >>> <environment: namespace:limma=""> > >>> > >>> > >>>> x<- as.matrix(e.qn) > >>>> batch<- as.factor(c(1,1,2,2,1,1,2,2,1,1,2,2,1,1,2,2)) > >>>> contrasts(batch)<- contr.sum(levels(batch)) > >>>> X<- model.matrix(~batch)[, -1, drop = FALSE] > >>>> qr.resid(qr(matrix(c(1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8),16,1)), X) > >>> batch1 > >>> 1 1 > >>> 2 1 > >>> 3 -1 > >>> 4 -1 > >>> 5 1 > >>> 6 1 > >>> 7 -1 > >>> 8 -1 > >>> 9 1 > >>> 10 1 > >>> 11 -1 > >>> 12 -1 > >>> 13 1 > >>> 14 1 > >>> 15 -1 > >>> 16 -1 > >>>> qr.resid(qr(matrix(c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2),16,1)), X) > >>> batch1 > >>> 1 1 > >>> 2 1 > >>> 3 -1 > >>> 4 -1 > >>> 5 1 > >>> 6 1 > >>> 7 -1 > >>> 8 -1 > >>> 9 1 > >>> 10 1 > >>> 11 -1 > >>> 12 -1 > >>> 13 1 > >>> 14 1 > >>> 15 -1 > >>> 16 -1 > >>>> qr.resid(qr(matrix(1,16,1)), X) > >>> batch1 > >>> 1 1 > >>> 2 1 > >>> 3 -1 > >>> 4 -1 > >>> 5 1 > >>> 6 1 > >>> 7 -1 > >>> 8 -1 > >>> 9 1 > >>> 10 1 > >>> 11 -1 > >>> 12 -1 > >>> 13 1 > >>> 14 1 > >>> 15 -1 > >>> 16 -1 > >>> > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >> -- > >> James W. MacDonald, M.S. > >> Biostatistician > >> Douglas Lab > >> University of Michigan > >> Department of Human Genetics > >> 5912 Buhl > >> 1241 E. Catherine St. > >> Ann Arbor MI 48109-5618 > >> 734-615-7826 > >> > >> ********************************************************** > >> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > [[alternative HTML version deleted]]
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