Question

Begginig doubts about layout and toptable

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Marcelo Luiz de Laia ▴ 770

@marcelo-luiz-de-laia-377

Last seen 10.2 years ago

Hi everyone. I use the Imagene out put file. I analyse it in limma very well, but I have a doubt in layout. In the limma manual, layout are acquired by the getLayout(GAL) function. In my case, I include layout by "hand", using the list, for exemplo: layout=list(ngrd.r=4,...). Have another hand (way) to enter layout in layout? Another doubt: In the limma manual have to type of toptable: 1. topTable(fit, n=30, adjust="fdr") in this type I have a error. 2. toptable(number=30,genelist=gal,fit=fit,eb=eb,adjust="fdr") in this case I have a error because I dont have the gal file. How do I do to fit genelist in my case (imagene out put file). Thanks Marcelo ---

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ADD COMMENT • link updated 21.1 years ago by Pete ▴ 70 • written 21.1 years ago by Marcelo Luiz de Laia ▴ 770

score 0 · Answer 1 · 2003-10-23

> Hi everyone. > > I use the Imagene out put file. > > I analyse it in limma very well, but I have a doubt in layout. > > In the limma manual, layout are acquired by the getLayout(GAL) function. In > my case, I include layout by "hand", using the list, for exemplo: > layout=list(ngrd.r=4,...). Have another hand (way) to enter layout in > layout? if your raw data was read in to RG then you can use layout<-RG$printer > > Another doubt: > > In the limma manual have to type of toptable: > > 1. topTable(fit, n=30, adjust="fdr") > in this type I have a error. > > 2. toptable(number=30,genelist=gal,fit=fit,eb=eb,adjust="fdr") > in this case I have a error because I dont have the gal file. > > How do I do to fit genelist in my case (imagene out put file). Again if your data is in RG use genes<-RG$genes toptable(number=30, genelist=genes, fit=fit, eb=eb, adjust="fdr") Hope that helps Pete Underhill Microarray Facility MRC Harwell