I am analyzing the variance sources of TCGA expression data using variancePartition. I want to check among others the effect of individuals in the variance, but when I specify it at the formula, I get the following errors:
> form <- ~ submitter_id > varPart <- fitExtractVarPartModel(Filt_EXP1, form, clin) Error in checkModelStatus(fit, showWarnings = showWarnings, colinearityCutoff) : Colinear score = 1 > 0.999 Covariates in the formula are so strongly correlated that the parameter estimates from this model are not meaningful. Dropping one or more of the covariates will fix this problem > form <- ~ (1|submitter_id) > varPart <- fitExtractVarPartModel(Filt_EXP1, form, clin) Error: number of levels of each grouping factor must be < number of observations > form <- ~ (0|submitter_id) > varPart <- fitExtractVarPartModel(Filt_EXP1, form, clin) Error in (function (cl, name, valueClass) : assignment of an object of class “numeric” is not valid for @‘Dim’ in an object of class “dgTMatrix”; is(value, "integer") is not TRUE
I can see why the above return an error, but at the vignette effect of individuals can be tested for. Is it a specific way I should specify it?
Thanks in advance.