Dear Gordon,

Thanks for clarifying this. My followup question will then regard the
rownames of the topTable output.

If I use topTable with only an input, the table looks fine.
But if I use the argument coef=1, the rownames disappear.
See my example (using limma_3.17.3):

> rownames(fitContrasts$coefficients)[1:5]
[1] "1769308_at" "1769311_at" "1769312_at" "1769313_at" "1769314_at"
> rownames(topTable(fitContrasts))[1:5]
[1] "1774122_at" "1775717_at" "1779660_at" "1770580_at" "1771091_at"
> rownames(topTable(fitContrasts,coef=1))[1:5]
[1] "2492" "655"  "5398" "5090" "2233"

Is this also intended?
Sorry if I am making an obvious mistake.

Kind regards
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


On Thu, Apr 18, 2013 at 2:25 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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://www.stat.math.ethz.ch/pipermail/bioconductor/2013-April/052127.html>
> https://stat.ethz.ch/**pipermail/bioconductor/**
> attachments/20130415/b0009b65/**attachment.pl<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
>> Office: +46 (0)31 772 38 86
>> Fax: +46 (0)31 772 38 01
>> Room: 3057B
>> www.sysbio.se
>> www.chalmers.se
>>
>>
> ______________________________**______________________________**__________
> The information in this email is confidential and inte...{{dropped:9}}

