[BioC] limma genedata

[Matthew Ritchie]

Hi Dennis,

> Hello all,
> Thankyou for your suggestions yesterday (re: getting started), they 
> were extremely helpful. Now I have a more specific question about the 
> limma User's guide. In section 8.2 on the 2-sample w/reference method, 
> the plot commands reference an object "genelist" that points nowhere 
> for me. I have to delet the item to get the command to work, and this 
> causes results to be returned absent identifiers. I'm referring to the 
> following command:
>
> toptable(coef=2,number=15,genelist=genelist[,1:6],fit=fit,eb=eb,adjust="fdr") 
>
>
> ? Can I replace
>
> genelist=genelist[,1:6]
>
> with
> genelist=RG$genes
> or something similar? 


Yes, this should work fine.  If you have duplicate spots on your arrays, 
and have used them in the linear model fit (ie ndups=2, etc in lmFit() 
), you'll need to adjust your genelist using uniquegenelist() so that 
the number of rows (genes) of the genelist argument in toptable() agrees 
with the number of rows (genes) in the fit argument (otherwise the names 
toptable() gives you won't be right).

Best wishes,

Matt Ritchie

> It seems to be necessary to get the names of the genes in the output 
> from Bayes analysis. I am using a non-model organism with some cDNA 
> libs of my own construction, so only a fraction of the clones are 
> sequenced and the rest have clone ID's.
> By the way, most of the image links in the LIMMA User's Guide are broken.
> -Dennis
> p.s. I'm working from a debian linux platform.