[BioC] Fwd: ComBat_ Error in solve.default(t(design) %*% design) : Lapack routine dgesv: system is exactly singular

[Dr J. Peters]

Dear Amit,

I suspect this may be occurring because your batches and covariate 
(malaria severity) are highly correlated, so ComBat is unable to 
distinguish the batch effects and the biological effect you wish to 
preserve.

Best wishes

Jimmy


> 
> ------------------------------
> 
> Message: 6
> Date: Mon, 19 Aug 2013 11:45:36 +0530
> From: amit kumar subudhi <amit4help at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Fwd: ComBat_ Error in solve.default(t(design) %*%
> 	design) : Lapack routine dgesv: system is exactly singular: U[4, 4] =
> 	0
> Message-ID:
> 	<CADxjrxV9MnzNV+WUaF+eJ2eFc1kqLjFgX_LefuxLRgCX6TvXvg at mail.gmail.com>
> Content-Type: text/plain
> 
> Hello to all ComBat users and to Dr. Evan,
> 
> I am trying to remove the batch effects from some of my microarray data 
> but
> at last I am getting an error message which read as
> 
> Found 3 batches
> Found 1  categorical covariate(s)
> Standardizing Data across genes
> Error in solve.default(t(design) %*% design) :
>   Lapack routine dgesv: system is exactly singular: U[4,4] = 0
> 
> The head(edata) looks like this
>                                  AL        AO        AP        AQ       
>  CF
> GT_pfalci_specific_0000001 16.053898 16.080540 16.101114 16.046898 
> 16.087206
> GT_pfalci_specific_0000002 10.051407 10.477143  8.369233 10.657850 
> 13.312936
> GT_pfalci_specific_0000003  8.910620  8.683393  7.812817  8.496099 
> 10.920685
> GT_pfalci_specific_0000004  6.603195  8.993232  6.476777  6.792369  
> 3.319346
> GT_pfalci_specific_0000005  9.813562 11.084574  9.055613 11.568550 
> 12.977261
> GT_pfalci_specific_0000006 15.989252 15.993513 15.963054 16.000675 
> 15.983985
>                                   CL        CU        CV     GA_UC     
> GB_UC
> GT_pfalci_specific_0000001 16.082037 16.071299 16.090370 15.971335 
> 15.994304
> GT_pfalci_specific_0000002 12.653076  9.703247  8.827624  5.697412  
> 8.060719
> GT_pfalci_specific_0000003 11.470758 10.548943 10.718349  6.132614  
> 8.007271
> GT_pfalci_specific_0000004  5.328515  8.398546  6.351136  3.045112  
> 3.891578
> GT_pfalci_specific_0000005  8.520699 11.791610 11.535907  6.791468  
> 9.930246
> GT_pfalci_specific_0000006 15.980660 15.984256 15.970124 13.353012 
> 13.740395
>                                GC_UC     GE_UC     GR_UC
> GT_pfalci_specific_0000001 15.855644 16.090246 16.086956
> GT_pfalci_specific_0000002  9.026398  8.015609  7.814614
> GT_pfalci_specific_0000003  5.341252  8.658231  5.788790
> GT_pfalci_specific_0000004  4.191565  3.040515  3.517175
> GT_pfalci_specific_0000005  5.446910 11.982848  5.477334
> GT_pfalci_specific_0000006 11.872469 13.675290 13.117105
> 
> GT_pfalci_specific_0000006 15.983985 15.970124
> 
> and the head(pheno) looks like this
>   sample batch malaria
> AL      1     1  severe
> AO      2     1  severe
> AP      3     1  severe
> AQ      4     1  severe
> CF      5     2  severe
> CL      6     2  severe
> 
> 
> the commands that I have used for ComBat is
> mod = model.matrix(~as.factor(malaria), data=pheno)
> combat_edata = ComBat(dat=edata, batch=batch, mod=mod, numCovs=NULL,
> par.prior=TRUE, prior.plots=FALSE)
> 
> head(mod) looks like this
>    (Intercept) as.factor(malaria)uncomplicated
> AL           1                               0
> AO           1                               0
> AP           1                               0
> AQ           1                               0
> CF           1                               0
> CL           1                               0
> 
> Why I am getting this error meassage? Please help me out. When I am 
> taking
> the larger sample size (n=33) I could able to remove the batch effects
> without an error message but a subset of those samples giving me the 
> above
> problem. I have gone through the Combat user group forum and could able 
> to
> see that one or two users faced the same problem but I could not 
> rectify it
> after following suggestions in those posts. Please help me out.
> 
> With best regards
> Amit
> 
> 
> --
> Amit Kumar Subudhi
> Research Scholar,
> CSIR-Senior Research Fellow,
> Molecular Parasitology and Systems Biology Lab,
> Department of Biological Sciences ,
> FD III, BITS, Pilani,
> Rajasthan- 333031
> e mail-
> amit4help at gmail.com
> amit.subudhi at pilani.bits-pilani.ac.in
> Mob No- 919983525845
> 
> 
> 
> 
> --
> Amit Kumar Subudhi
> Research Scholar,
> CSIR-Senior Research Fellow,
> Molecular Parasitology and Systems Biology Lab,
> Department of Biological Sciences ,
> FD III, BITS, Pilani,
> Rajasthan- 333031
> e mail-
> amit4help at gmail.com
> amit.subudhi at pilani.bits-pilani.ac.in
> Mob No- 919983525845
> 
> 
> 
> 
> --
> Amit Kumar Subudhi
> Research Scholar,
> CSIR-Senior Research Fellow,
> Molecular Parasitology and Systems Biology Lab,
> Department of Biological Sciences ,
> FD III, BITS, Pilani,
> Rajasthan- 333031
> e mail-
> amit4help at gmail.com
> amit.subudhi at pilani.bits-pilani.ac.in
> Mob No- 91998352584
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> End of Bioconductor Digest, Vol 126, Issue 18
> *********************************************