Coefficients not estimable voom Lima with multiple numeric covariate
1
0
Entering edit mode
Will • 0
@will-23665
Last seen 2.8 years ago
Italy

Hi, I have a DGEList x containing genes in rows and samples in columns (multiple samples for same patient). I have no NA in my data because I used complete.case function(). I create the design matrix in this way:

design <- model.matrix(~0 + f1  + f2  + f3 + f4 + f5 + f6 + f7 + f8 + f9 + age + gender, data=x$samples)

where f are some features (in this case I have 9 features). These are just numeric vector not factor, so in the design matrix each feature has only one single column (equal for age). Instead gender is a factor (M or F). So in the design matrix it has 2 columns.

When I Call:

v    <- voom(x, design, plot = F)

it returns:

Coefficients not estimable: f7 f8 f9 age genderF genderM
Warning message: Partial NA coefficients for 17080 probe(s) I see that it's ok until the totale value passed to model.matrix are 6 no more.

Why ??

When I call: vfit <- lmFit(v, design) it returns the same warning and the columns corresponding (f7 f8 f9 age genderF genderM) in the vift$coefficents are only with NA. I see that passing 6 parameters in the model.matrix is ok, but no more 6.

r limma design rnaseq voom • 764 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 6 hours ago
WEHI, Melbourne, Australia

The warning is telling you that the covariates are co-linear. It is impossible to identify coefficients for co-linear variables because of ambiguity between them. The more covariates you add the more chance one of them will be co-linear with the others.

In general, it is very difficult to get unambiguous results when including so many variables in a linear model. I have never seen myself an expression dataset for so many variables would be appropriate.

ADD COMMENT

Login before adding your answer.

Traffic: 974 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6