[BioC] lmFit not keeping rownames of arg object?

[Gordon K Smyth]

Dear Leif,

I've cc'd to the Bioconductor mailing list because this will be of 
interest to others.

Yes, this is an intended update.  The rownames are passed on, but as 
rownames of fit$coefficients, rather than as a column in the $genes 
component.

If you use topTable() you will see that the rownames of object are now 
preserved as rownames of the output table.  This is new in limma 3.17.3.

See the recent discussion:

https://www.stat.math.ethz.ch/pipermail/bioconductor/2013-April/052127.html
https://stat.ethz.ch/pipermail/bioconductor/attachments/20130415/b0009b65/attachment.pl

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth

On Wed, 17 Apr 2013, Leif Väremo wrote:

> Dear Gordon,
>
> In the limma function lmFit, the output object contains an element $genes
> which is the rownames of the input argument 'object'. This is true for
> version 3.16.0.
>
> However in the current devel version (3.17.3) the rownames seem not to be
> passed, and the $genes element is simply NULL.
>
> Is this an intended update or will it be fixed?
>
> Sincerely,
> Leif
> ____________________________________________________
>
> *Leif Väremo*,* *PhD student
>
> *Systems and Synthetic Biology*
> Department of Chemical and Biological Engineering
> Chalmers University of Technology
> Kemivägen 10, SE-412 96 Göteborg
>
> Mobile: +46 (0)705 44 26 43
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