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? 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.

At 06:22 AM 12/03/2004, Dennis Hazelett wrote: >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,adjus t="fdr") > >? Can I replace > >genelist=genelist[,1:6] > >with >genelist=RG$genes >or something similar? Yes of course. But here's two hints. Firstly, in the versions of limma since Christmas, limma is now setting the genelist information directly from Genepix gpr files. So you don't have to bother with reading the GAL file. Secondly, you can now use lmFit instead of lm.series, and then simply topTable(fit) will find the gene names correctly. See the swirl case study for an example of this. > 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. This is news to me - I have never heard of this happening before. Please advise me off the list the details of your operating system and limma version and tell me what's happening exactly. Gordon >-Dennis >p.s. I'm working from a debian linux platform.

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,adju st="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.