Question: variancePartition - testing for individuals

0

rina •

**0**wrote:Hi all!

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.

R.

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modified 23 days ago
by
mikhael.manurung •

**10**• written 24 days ago by rina •**0**