Question: Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
0
gravatar for michael.zulyniak
5.0 years ago by
Canada
michael.zulyniak0 wrote:

Hello,

I've begun processing Methylation450 data using them infi package. The operation has been flawless through data input: (read.450k.exp), phenotype table (pData), Illumina background normalization (preprocessIllumina), and SWAN normalization (preprocessSWAN). However, I am some difficulty with dmpFinder that I cannot figure out or find on any chat/help forums other than 'Iimma' but they have not provided a solution.

After successfully creating a SWAN normalized dataset I'm ready to find differentially methylated regions between individuals at the start and end of a trial (e.g.,"0" and "1") using dmpHunter. However, I am getting an error that I cannot solve: Error in lm.fit(design, t(M)) : incompatible dimensions. Here is my process that produces the error.

>pd1 <- pData(RGset)

>Mset.swan <- preprocessSWAN(RGset, MSet.norm)

>M <- getM(Mset.swan, type = "beta", betaThreshold = 0.001)

>dmpTimePoint <- dmpFinder(M, pheno=pd1$TimePoint, type = "categorical")

Error in lm.fit(design, t(M)) : incompatible dimensions

 

At first I thought the issue was with the dimensions of 'M' or 'pd', but they're both 168:

> dim(M)
[1] 485512    168
> dim(pd)
[1] 168  17

I then tried removing any 'NA' values in 'pd' but that resulted in the same error message:

Error in lm.fit(design, t(M)) : incompatible dimensions

 

As requested, here is the output for the sessionInfo() command:

R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GPArotation_2012.3-1                                  
 [2] psych_1.4.8.11                                        
 [3] minfiData_0.3.4                                       
 [4] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3
 [5] IlluminaHumanMethylation450kmanifest_0.4.0            
 [6] minfi_1.6.0                                           
 [7] Biostrings_2.28.0                                     
 [8] GenomicRanges_1.12.5                                  
 [9] IRanges_1.18.4                                        
[10] reshape_0.8.5                                         
[11] lattice_0.20-29                                       
[12] Biobase_2.20.1                                        
[13] BiocGenerics_0.6.0                                    

loaded via a namespace (and not attached):
 [1] beanplot_1.1          grid_3.0.1            illuminaio_0.2.0     
 [4] limma_3.16.8          MASS_7.3-34           matrixStats_0.10.0   
 [7] mclust_4.3            multtest_2.16.0       nor1mix_1.2-0        
[10] plyr_1.8.1            preprocessCore_1.22.0 R.methodsS3_1.6.1    
[13] RColorBrewer_1.0-5    Rcpp_0.11.2           siggenes_1.34.0      
[16] splines_3.0.1         stats4_3.0.1          survival_2.37-7      
[19] tools_3.0.1          

 

 

Thank you in advance, any and all help would be greatly appreciated.

 

Sincerely,

Mike Zulyniak

McMaster University

ADD COMMENTlink modified 5.0 years ago by James W. MacDonald51k • written 5.0 years ago by michael.zulyniak0
Answer: Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
0
gravatar for James W. MacDonald
5.0 years ago by
United States
James W. MacDonald51k wrote:
Hi Michael, That's a weird error, given that dmpFinder() ensures that the the length of your pheno vector is equal to the number of columns in M: n <- length(pheno) if (n != ncol(M)) stop("length of pheno does not equal number of samples") Without knowing more about your M and pheno arguments, you will have to debug yourself: debug(dmpFinder) dmpTimePoint <- dmpFinder(M, pheno=pd1$TimePoint, type = "categorical") Then step through the function until you get to the lines (right near the beginning) if (type == "categorical") { pheno <- factor(as.character(pheno)) design <- model.matrix(~pheno) fit <- lmFit(M, design) and check the dimensions of M and the design matrix, because they are obviously not compatible at that point. Best, Jim On Thu, Sep 18, 2014 at 2:31 PM, michael.zulyniak on Biostar < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User michael.zulyniak <https: support.bioconductor.org="" u="" 6748=""/> wrote Question: > Help with function 'dmpFinder' in minfi library > <https: support.bioconductor.org="" p="" 61544=""/>: > > Hello, > > I've begun processing Methylation450 data using them infi package. The > operation has been flawless through data input: (read.450k.exp), phenotype > table (pData), Illumina background normalization (preprocessIllumina), and > SWAN normalization (preprocessSWAN). However, I am some difficulty with *dmpFinder > *that I cannot figure out or find on any chat/help forums other than > 'Iimma' but they have not provided a solution. > > After successfully creating a SWAN normalized dataset I'm ready to find > differentially methylated regions between individuals at the start and end > of a trial (e.g.,"0" and "1") using dmpHunter. However, I am getting an > error that I cannot solve. > > *>pd1 <- pData(RGset)* > > *>Mset.swan <- preprocessSWAN(RGset, MSet.norm)* > > *>M <- getM(Mset.swan, type = "beta", betaThreshold = 0.001)* > > *>dmpTimePoint <- dmpFinder(M, pheno=pd1$TimePoint, type = "categorical")* > > *Error in lm.fit(design, t(M)) : incompatible dimensions* > > > > At first I thought the issue was with the dimensions of 'M' or 'pd', but > they're both 168: > > > > > *> dim(M) [1] 485512 168 > dim(pd) [1] 168 17* > > I then tried removing any 'NA' values in 'pd' but that resulted in the > same error message: > > *Error in lm.fit(design, t(M)) : incompatible dimensions* > > > > As requested, here is the output for the sessionInfo() command: > > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] GPArotation_2012.3-1 > [2] psych_1.4.8.11 > [3] minfiData_0.3.4 > [4] IlluminaHumanMethylation450kannotation.ilmn.v1.2_0.1.3 > [5] IlluminaHumanMethylation450kmanifest_0.4.0 > [6] minfi_1.6.0 > [7] Biostrings_2.28.0 > [8] GenomicRanges_1.12.5 > [9] IRanges_1.18.4 > [10] reshape_0.8.5 > [11] lattice_0.20-29 > [12] Biobase_2.20.1 > [13] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] beanplot_1.1 grid_3.0.1 illuminaio_0.2.0 > [4] limma_3.16.8 MASS_7.3-34 matrixStats_0.10.0 > [7] mclust_4.3 multtest_2.16.0 nor1mix_1.2-0 > [10] plyr_1.8.1 preprocessCore_1.22.0 R.methodsS3_1.6.1 > [13] RColorBrewer_1.0-5 Rcpp_0.11.2 siggenes_1.34.0 > [16] splines_3.0.1 stats4_3.0.1 survival_2.37-7 > [19] tools_3.0.1 > > > > > > Thank you in advance, any and all help would be greatly appreciated. > > > > Sincerely, > > Mike Zulyniak > > McMaster University > > ------------------------------ > > You may reply via email or visit Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.0 years ago by James W. MacDonald51k

Hi Jim,

Thanks for the reply. I'll give it shot and let you know how it turns out. The debug() function is a new one to me but certainly makes sense as a good place to start.

I'll let you know how it turns out.

Mike

ADD REPLYlink written 5.0 years ago by michael.zulyniak0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 203 users visited in the last hour