Question: Extracting expressions after a multtest procedure (part2)
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gravatar for JUAN MIGUEL MARIN DIAZARAQUE
11.7 years ago by
Hello, I think this is a valuable information. Best ----- Mensaje reenviado de jmmarin at est-econ.uc3m.es ----- Fecha: Mon, 17 Mar 2008 23:59:59 +0100 De: "J. Miguel Marin" <jmmarin at="" est-econ.uc3m.es=""> Responder-A: "J. Miguel Marin" <jmmarin at="" est-econ.uc3m.es=""> Asunto: Re: [BioC] Extracting expressions after a multtest procedure (part2) Para: Martin Morgan <mtmorgan at="" fhcrc.org=""> Hello Martin, you are absolutely right. In fact, I need to identify just the correct genes because I am searching for significant differences in expressions in order to calculate distances among the same genes in "BCR/ABL" group and in "NEG" group. Thank you very much again for your help. Best. > JUAN MIGUEL MARIN DIAZARAQUE wrote: >> Helo Martin, >> >> In fact when I wrote >> >>> idx1 = res$index[res$adjp[,"BH"]<0.05,] >> Error in res$index[res$adjp[, "BH"] < 0.05, ] : incorrect number of >> dimensions > > I guess that should have been idx1=res$index[ res$adjp[,"BH"]<0.05] ] > > I know that Sean's suggestion works, in the sense that you get an > answer. I was not quite sure that it was the right answer -- res$adjp > is ordered from highest significance to lowest significance. When you > > idx2 = res$adjp[,"BH"]<0.05 > > you get a logical vector (TRUE and FALSE values), probably all the > first ones are TRUE and all the later ones FALSE (because adjp was > ordered that way). > > > head(idx2, n=110) > [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [25] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [37] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [49] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [73] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [85] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > [97] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE > [109] FALSE FALSE > > Now when you subset exprs(esetSub)[idx2,], you select all the rows of > exprs(esetSub) for which the corresponding entry in idx2 is 'TRUE'. > But since the order of genes in res$adjp is different from the order > of genes in exprs(esetSub), you won't get the right genes. > > Martin > >> Anyway, thank you very much for your help. >> >> Cheers >> >>> Off list, because I am not sure, but from the docs I think there >>> might be a couple of redirections >>> >>> idx1 = res$index[res$adjp[,"BH"]<0.05,] >>> >>> to get to resT[idx,], and maybe a second (or using the rownames) to >>> get back to the ExpressionSet. >>> >>> If you figure it out, Juan, and if there is a correction, it would >>> be good to post to the list again. >>> >>> Martin >>> >>> Sean Davis wrote: >>>> On Sun, Mar 16, 2008 at 11:56 AM, JUAN MIGUEL MARIN DIAZARAQUE >>>> <jmmarin at="" est-econ.uc3m.es=""> wrote: >>>>> Hello, >>>>> >>>>> In previous message I wonder how to extract just the expressions of 102 >>>>> genes under two conditions after a multtest procedure. >>>>> >>>>> At last, I wrote this unelegant code that seems to work: >>>>> >>>>> quedan <- resT[res$adjp[,"BH"]<0.05,] >>>>> busco <- dimnames(quedan)[[1]] >>>>> >>>>> cosa <- NULL >>>>> for (i in 1:length(dimnames(exprs(esetSub))[[1]])) >>>>> for (j in 1:length(busco)) >>>>> if (dimnames(exprs(esetSub[i,]))[[1]] == busco[j]) { >>>>> cosa <- rbind(cosa, as.data.frame(exprs(esetSub))[i,]) } >>>>> end >>>>> end >>>> >>>> Generally, you can subset ExpressionSets just like you do data frames; >>>> rows are genes or probes and columns are samples. If esetSub is what >>>> you used for your multtest procedure, you should be able to do: >>>> >>>> exprs(esetSub)[res$adjp[,'BH']<0.05,] >>>> >>>> In general, for loops are quite useful in R, but for things like >>>> subsetting or vectorized operations, it is better to look for other >>>> alternatives as they are likely to be faster. >>>> >>>> Sean >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> >> >> >> jm~ >> >> _______________________________ >> >> Juan Miguel Marin >> >> http://www.est.uc3m.es/jmmarin >> >> Dep. of Statistics >> University Carlos III of Madrid >> Spain (E.U.) >> _______________________________ >> >> > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > jm~ _______________________________ J. Miguel Marin http://www.est.uc3m.es/jmmarin Dep. of Statistics University Carlos III of Madrid Spain (E.U.) _______________________________ ----- Terminar mensaje reenviado -----
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