Combat in R (SVA package) error message
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kimyoorin1 • 0
@kimyoorin1-7769
Last seen 6.4 years ago
United States

Hi, 

Basically we have a spreadsheet containing all our microarray data, genes in rows and samples in colums. We have 6 batches in total, each containing 5-8 samples (53 samples in total) that were run on 5 different microarrays. I also created a SIF.csv file containing 3 columns : Array, Sample, Batch (See head and tail below). Array goes from 1 to 6, Batch goes from 1 to 6 and sample contains the name of each sample (same as in the spreadsheet). When running combat it generates some error.. The tutorial and manual is custom for a certain type of data and didn't help me understand how to apply this to more universal type of data. I don't understand how to get run combat, it constantly generates errors. What am I doing wrong with the script below? 

> head(sif)
   Array            Sample   Batch
1 Array1           Sample1  Batch1
2 Array1           Sample2  Batch1
3 Array1           Sample3  Batch1
4 Array1           Sample4  Batch1
5 Array1           Sample5  Batch1
6 Array1           Sample6  Batch1

> tail(sif)
    Array      Sample  Batch
48 Array6    Sample48 Batch6
49 Array6    Sample49 Batch6
50 Array6    Sample50 Batch6
51 Array6    Sample51 Batch6
52 Array6    Sample52 Batch6
53 Array6    Sample53 Batch6

 

> library(sva)

> dat = read.csv("Combat_matrix_input.csv");
> sif = read.csv("sif.csv");
> modcombat = model.matrix(~1, data=dat)

# Here I run combat as per the tutorial
> combat_edata = ComBat(dat, batch=batch, mod=modcombat, par.prior=TRUE, prior.plots=FALSE)
Found 6 batches
Error in cbind(batchmod, mod) : 
  number of rows of matrices must match (see arg 2)

#I was suspecting that the error was coming from mod, so I set it to NULL
> combat_edata = ComBat(dat, batch=batch, mod=NULL, par.prior=TRUE, prior.plots=FALSE)
Found 6 batches
Adjusting for 0 covariate(s) or covariate level(s)
Standardizing Data across genes
Error in solve(t(design) %*% design) %*% t(design) %*% t(as.matrix(dat)) : 
  requires numeric/complex matrix/vector arguments

 

combat software error • 4.0k views
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@peter-langfelder-4469
Last seen 14 months ago
United States
The first error is thrown because modcombat has wrong dimensions, you should have used modcombat = model.matrix(~1, data=sif) i.e., modcombat should have as many rows as samples, not genes. Without seeing all the data it is difficult to say why ComBat is throwing the second error but I suspect that some columns in 'dat' are not numeric. Try mode(as.matrix(dat)) and if you get anything else than "numeric", the problem is that the data in dat are not all numeric. Hope this helps, Peter On Tue, May 19, 2015 at 12:09 PM, kimyoorin1 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User kimyoorin1 wrote Question: Combat generates error message: > > Hi, > > Basically we have a spreadsheet containing all our microarray data, genes in > rows and samples in colums. We have 6 batches in total, each containing 5-8 > samples (53 samples in total) that were run on 5 different microarrays. I > also created a SIF.csv file containing 3 columns : Array, Sample, Batch (See > head and tail below). Array goes from 1 to 6, Batch goes from 1 to 6 and > sample contains the name of each sample (same as in the spreadsheet). When > running combat it generates some error.. The tutorial and manual is custom > for a certain type of data and didn't help me understand how to apply this > to more universal type of data. I don't understand how to get run combat, it > constantly generates errors. What am I doing wrong with the script below? > >> head(sif) > Array Sample Batch > 1 Array1 Sample1 Batch1 > 2 Array1 Sample2 Batch1 > 3 Array1 Sample3 Batch1 > 4 Array1 Sample4 Batch1 > 5 Array1 Sample5 Batch1 > 6 Array1 Sample6 Batch1 > >> tail(sif) > Array Sample Batch > 48 Array6 Sample48 Batch6 > 49 Array6 Sample49 Batch6 > 50 Array6 Sample50 Batch6 > 51 Array6 Sample51 Batch6 > 52 Array6 Sample52 Batch6 > 53 Array6 Sample53 Batch6 > > > >> library(sva) > >> dat = read.csv("Combat_matrix_input.csv"); >> sif = read.csv("sif.csv"); >> modcombat = model.matrix(~1, data=dat) > > # Here I run combat as per the tutorial >> combat_edata = ComBat(dat, batch=batch, mod=modcombat, par.prior=TRUE, >> prior.plots=FALSE) > Found 6 batches > Error in cbind(batchmod, mod) : > number of rows of matrices must match (see arg 2) > > #I was suspecting that the error was coming from mod, so I set it to NULL >> combat_edata = ComBat(dat, batch=batch, mod=NULL, par.prior=TRUE, >> prior.plots=FALSE) > Found 6 batches > Adjusting for 0 covariate(s) or covariate level(s) > Standardizing Data across genes > Error in solve(t(design) %*% design) %*% t(design) %*% t(as.matrix(dat)) : > requires numeric/complex matrix/vector arguments > > > > ________________________________ > > You may reply via email or visit Combat in R (SVA package) error message
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I should also say that using model.matrix(~1,...) is equivalent to the default mod = NULL. Unless you have actual covariates, you can leave mod at the default value.

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