Limma Camera error
Last seen 5.8 years ago
I have done a differential expression analysis using limma. When I try the camera analysis
I get the error Error in U[iset, , drop = FALSE] : no 'dimnames' attribute for array
Here the voom_data is the voom output, design is what i use the design matrix in voom. all_signatures_for_camera is a list of 18 gene sets?
What is causing the error ?
Last seen 8 hours ago
WEHI, Melbourne, Australia
Are you using the latest release of Bioconductor and limma?
Please show us the output of these commands:
If you type this:
do you get an error?
Edit: I have now confirmed that this is a bug in camera(), which is not handling character index vectors correctly when observation weights are set. To avoid this, convert all the character index vectors to integer index vectors like this: integer_signatures <- ids2indices(all_signatures_for_camera, rownames(voom_data))
integer_signatures instead of
Edit 2: This bug has since been fixed in both the release and developmental versions of limma.
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