Hi to all, I have a microarray experiment with 10 different contrasts and I would like to generate a dataframe containing all the informations exported with the function toptable for all the the genes (no restrictions on p-value and logFC but with BH adjustment). For 1 specific contrast I proceed like that : res=toptable(coef=1,number=15120,fit=fit2,genelist=Ebgnorm$genes[isGen e,],adjust.method="BH",A=fit2$Amean,eb=fit2) res.summary=data.frame(res$ProbeUID,res$ProbeName,res$GeneName,res$Des cription,res$P.Value,res$adj.P.Val,res$logFC,exp(res$logFC*log(2))) and after I add to this dataframe the normalized log intensities and weights: lg=data.frame(Ebgnorm$genes$ProbeUID[isGene],Ebgnorm$genes$ProbeName[i sGene],Ebgnorm$E[isGene,],Ebgnorm$weights[isGene,]) res2=res.summary[order(res.summary$ProbeUID),] lg2=lg[order(lg$ProbeUID),] res2=cbind(res2,lg2[,3:18]) write.table(res2,file="result_Weights_and_Intensities.txt",sep="\t",qu ote=FALSE,col.names=TRUE,row.names=FALSE) It works very well for one contrast but now, I would like to do that for all the contrasts at the same time. I tried the functions write.fit and topTableF but, with the first one I cannot have the adjusted p-values and for the second one, there is only one column of adjusted p-value (with method="separate" and "global") and not one for each contrast. So, is there any other function to solve my problem or will I have to perform the exportation of all contrasts one by one and then concatenate them ? Thank in advance for your help. Benoit -- Benoit Loup, PhD UMR Biologie du D?veloppement et Reproduction Diff?renciation des Gonades et Perturbations INRA ? Domaine de Vilvert B?timent Jacques Poly 78350 Jouy en Josas France Tel: 33 1 34 65 25 38 Fax: 33 1 34 65 22 41 E-mail: benoit.loup at jouy.inra.fr

Quoting Benoit Loup <benoit.loup at="" jouy.inra.fr="">: > Hi to all, > > I have a microarray experiment with 10 different contrasts and I would > like to generate a dataframe containing all the informations exported > with the function toptable for all the the genes (no restrictions on > p-value and logFC but with BH adjustment). > > For 1 specific contrast I proceed like that : > res=toptable(coef=1,number=15120,fit=fit2,genelist=Ebgnorm$genes[isG ene,],adjust.method="BH",A=fit2$Amean,eb=fit2) > res.summary=data.frame(res$ProbeUID,res$ProbeName,res$GeneName,res$D escription,res$P.Value,res$adj.P.Val,res$logFC,exp(res$logFC*log(2))) > > and after I add to this dataframe the normalized log intensities and weights: > lg=data.frame(Ebgnorm$genes$ProbeUID[isGene],Ebgnorm$genes$ProbeName [isGene],Ebgnorm$E[isGene,],Ebgnorm$weights[isGene,]) > res2=res.summary[order(res.summary$ProbeUID),] > lg2=lg[order(lg$ProbeUID),] > res2=cbind(res2,lg2[,3:18]) > write.table(res2,file="result_Weights_and_Intensities.txt",sep="\t", quote=FALSE,col.names=TRUE,row.names=FALSE) > > It works very well for one contrast but now, I would like to do that > for all the contrasts at the same time. > I tried the functions write.fit and topTableF but, with the first one I > cannot have the adjusted p-values and for the second one, there is only > one column of adjusted p-value (with method="separate" and "global") > and not one for each contrast. > > So, is there any other function to solve my problem or will I have to > perform the exportation of all contrasts one by one and then > concatenate them ? > > Thank in advance for your help. > > Benoit Hi Benoit, I normally create a list with each individual contrast information (the result of 'topTable', not-ordered, so all probesets in teh same order) as a separate component. I like 'topTable' because it gives me all the info I want. Then I merely compile a large table by combining the columns containing first the annotation info, and then the different contrasts data (I normally just export the log2 ratios and adjusted p values at this stage). By putting them in a list you can automate the big table generation no matter how many contrasts you have. It may not be the most elegant form, but that's what I do. Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507095 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK ********************************************* Alternative email: nach.mcnach at gmail.com ********************************************* -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

Hi Benoit: > I tried the functions write.fit and topTableF but, with the first one > I cannot have the adjusted p-values ?write.fit ... Usage: write.fit(fit, results=NULL, file, digits=3, adjust="none", method="separate", F.adjust="none", sep="\t", ...) ... adjust: character string specifying multiple-testing adjustment method for the t-statistic P-values, e.g., ?"BH"?. See ?p.adjust? for the available options. If ?NULL? or ?"none"? then the P-values are not adjusted. It seems if you change the adjust parameter from "none", you should be able to get what you want. Best, Saroj > and for the second one, there is only one column of adjusted p-value > (with method="separate" and "global") and not one for each contrast. > > So, is there any other function to solve my problem or will I have to > perform the exportation of all contrasts one by one and then > concatenate them ? > > Thank in advance for your help. > > Benoit >