Hi Jordan, Sounds like a confounding issue. Are your covariates + batch linearly independent? In other words are there covariate levels or combinations that are nested within batch? Evan On Jan 16, 2014, at 12:54 PM, Jordan Ramsey wrote: > Hi there, > > I've been working with the ComBat function in the SVA package and I've found that there seems to be a problem when trying to include numerical covariates in the model. I consistently get the error: > > Error in t(design) %*% design : > requires numeric/complex matrix/vector arguments > > For example, if I run: > > model = model.matrix(~as.factor(Sex) + as.numeric(Age)) > ComBat_dat = ComBat(gene_express, batch = BatchNums, mod = model, numCovs = 3, prior.plots = TRUE) > > This produces: > Found 26 batches > Found 1 categorical covariate(s) > Found 1 continuous covariate(s) > Standardizing Data across genes > Error in t(design) %*% design : > requires numeric/complex matrix/vector arguments > > However, when I use a model that only includes factors, I don't get any errors. Any ideas on what is going wrong here? Any help would be appreciated. > > Thanks, > -- > Jordan Ramsey >

Hi Evan, I figured out what was going wrong - my batch variable was a character variable. This worked when all the covariates in the model were factors, but not when some were numerical. I changed the batch variable to a factor and it runs without errors now. Thanks, Jordan On Thu, Jan 16, 2014 at 7:27 PM, Johnson, William Evan <wej@bu.edu> wrote: > Hi Jordan, > > Sounds like a confounding issue. Are your covariates + batch linearly > independent? In other words are there covariate levels or combinations that > are nested within batch? > > Evan > > > On Jan 16, 2014, at 12:54 PM, Jordan Ramsey wrote: > > > Hi there, > > > > I've been working with the ComBat function in the SVA package and I've > found that there seems to be a problem when trying to include numerical > covariates in the model. I consistently get the error: > > > > Error in t(design) %*% design : > > requires numeric/complex matrix/vector arguments > > > > For example, if I run: > > > > model = model.matrix(~as.factor(Sex) + as.numeric(Age)) > > ComBat_dat = ComBat(gene_express, batch = BatchNums, mod = model, > numCovs = 3, prior.plots = TRUE) > > > > This produces: > > Found 26 batches > > Found 1 categorical covariate(s) > > Found 1 continuous covariate(s) > > Standardizing Data across genes > > Error in t(design) %*% design : > > requires numeric/complex matrix/vector arguments > > > > However, when I use a model that only includes factors, I don't get any > errors. Any ideas on what is going wrong here? Any help would be > appreciated. > > > > Thanks, > > -- > > Jordan Ramsey > > > > -- Jordan Ramsey PhD candidate (Biotechnology) Bahn Group Department of Chemical Engineering & Biotechnology University of Cambridge [[alternative HTML version deleted]]

Awesome news. Glad you figured it out! On Jan 16, 2014, at 3:33 PM, Jordan Ramsey wrote: Hi Evan, I figured out what was going wrong - my batch variable was a character variable. This worked when all the covariates in the model were factors, but not when some were numerical. I changed the batch variable to a factor and it runs without errors now. Thanks, Jordan On Thu, Jan 16, 2014 at 7:27 PM, Johnson, William Evan <wej@bu.edu<mailto:wej@bu.edu>> wrote: Hi Jordan, Sounds like a confounding issue. Are your covariates + batch linearly independent? In other words are there covariate levels or combinations that are nested within batch? Evan On Jan 16, 2014, at 12:54 PM, Jordan Ramsey wrote: > Hi there, > > I've been working with the ComBat function in the SVA package and I've found that there seems to be a problem when trying to include numerical covariates in the model. I consistently get the error: > > Error in t(design) %*% design : > requires numeric/complex matrix/vector arguments > > For example, if I run: > > model = model.matrix(~as.factor(Sex) + as.numeric(Age)) > ComBat_dat = ComBat(gene_express, batch = BatchNums, mod = model, numCovs = 3, prior.plots = TRUE) > > This produces: > Found 26 batches > Found 1 categorical covariate(s) > Found 1 continuous covariate(s) > Standardizing Data across genes > Error in t(design) %*% design : > requires numeric/complex matrix/vector arguments > > However, when I use a model that only includes factors, I don't get any errors. Any ideas on what is going wrong here? Any help would be appreciated. > > Thanks, > -- > Jordan Ramsey > -- Jordan Ramsey PhD candidate (Biotechnology) Bahn Group Department of Chemical Engineering & Biotechnology University of Cambridge [[alternative HTML version deleted]]