[BioC] limma with missing values
Gordon K Smyth
smyth at wehi.EDU.AU
Tue Mar 11 00:11:39 CET 2008
On Sat, 8 Mar 2008, Hans-Ulrich Klein wrote:
>> limma treats missing values in exactly the same way as other linear model
>> function in R, such as lm(), glm() etc. For each gene, the rows with
>> missing values are removed both from the data and design matrix, then
>> non-estimable coefficients are removed (given NA) from the end of the
>> design matrix.
> The problem is that often a user will not notice when limma drops a column of
> the design matrix for a few of many thousand genes. Maybe a warning message
> should be printed?
I have now added a warning message to lmFit() in this situation.
More information about the Bioconductor