On Wed, Apr 9, 2008 at 4:07 PM, Laura Bonnett <[EMAIL PROTECTED]> wrote: > Dear Sirs, > > I am using both the Bioconductor adds on (Affy, AffyPLM,...) and the > 'standard' R-package. > > I am trying to select a list of genes which all have expression values below > a certain threshold. > I have done this by creating a vector which has 0s where the expression is > greater than the threshold and 1s where it is less than or equal to it. > Multiplying this vector by the expression values produces a list of 0s and > expression values below the threshold value. > > However, now I need to remove the 0s. I thought that this would be > relatively trivial but it appears it isn't!!! >
Without a working example from you, I have no way to test this proposal. But if I were you, I would get the index values of the right cases in one step, and then use that to choose the ones I want. theGoodOnes <- which(exp2 >= 0) exp3 <- exp2[theGoodOnes] This can be crammed into one line, but I'd do it in two just to make sure it is correct, at least the first time. My example: > x <- rnorm(100) > which(x >= 0) [1] 9 11 12 13 14 16 19 20 21 22 24 25 28 30 32 34 35 36 38 40 41 42 43 44 46 [26] 47 49 50 53 54 57 59 61 63 64 66 68 69 70 72 75 78 80 81 82 83 88 90 97 98 > theGoodOnes <- which(x>=0) > newX <- x[theGoodOnes] > newX [1] 0.89285908 0.51753998 1.18485887 2.10003705 0.54535841 1.28313738 [7] 1.34092172 0.76064356 0.02201121 0.80808363 0.04578730 0.23045983 [13] 1.04306626 0.12694184 0.89706863 0.86302992 1.53471660 0.51192410 [19] 1.00366834 1.76923470 0.49508470 1.27888454 0.76706729 1.46340483 [25] 1.69315538 0.50537603 0.18422329 0.72968629 0.45490526 2.18208183 [31] 0.71926926 0.68915832 1.49076770 0.48763971 0.39273110 0.80709549 [37] 0.22099019 0.38103757 0.14626929 0.63933750 1.26643194 3.33091910 [43] 2.50341609 2.05286611 0.31986095 0.64548972 0.34712937 0.04075135 [49] 0.07206342 0.20325505 -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.