Error: dim(X) must have a positive length about honeybadger

[JEFworks]

Hi Roman,

Thanks for trying out HoneyBADGER!

I believe the error is due to the data being from mouse. A number of default options have been set under the assumption that the data is from human. For example, hb$setGexpMats has an id parameter that is by default 'hgnc_symbol'.

You will want to specify 'mgi_symbol' in your case assuming that the rownames in your matrix.sample are indeed MGI symbols. You can specify other biomaRt identifiers if your rownames are ENSEMBL or something else:

hb$setGexpMats(matrix.sample, matrix.ref, mart.obj, 
    filter=FALSE, scale=FALSE, verbose=TRUE, id='mgi_symbol')

setGexpMat then uses this id and your mart.obj to map genes to their genomic positions in the chromosome. You can double check that this is being done properly by looking at hb@gene; it should contain a GenomicRanges representation of genomic positions for all your genes.

Now, hb$plotGexpProfile() should be able to organize the genes by their genomic positions and make the appropriate visualization.

You can learn more about each function using and their default parameters:

?setGexpMats

Let me know if this fixes the issue.

Best,
Jean

[romanhaa]

That worked, thanks a lot! I guess I should've checked the additional parameters :)