This was due to an redesign of the EBImage data structure. This is fixed in the latest aroma.affymetrix which supports both the old and the new EBImage style. From the NEWS:
Package: aroma.core =================== Version: 1.1.0 [2009-05-29] [snip] o BUG FIX: Our internal interleave() for Image (defined by EBImage) gave 'Error in z[idxOdd,, ] : incorrect number of dimensions'. This was because internal image structure of the Image class changed (back) to being a 2-dim array. Now interleave() handles both 2d and 3d arrays. /Henrik On Wed, Apr 8, 2009 at 11:47 AM, Randy Gobbel <randy.gob...@gmail.com> wrote: > > [Apologies for the previous version -- Assay Explorer was a software > product from a company I used to work for. Brain fade. I'm hoping > there's a way to delete my previous post. -Randy] > > I'm trying to run through the workflow for FIRMA analysis of data from > Affymetrix HuEx arrays (HuEx-1_0-st-v2), detailed in the "Human Exon > Array Analysis" vignette at > http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis. > I get through the FIRMA analysis without problems, but my attempts to > use ArrayExplorer for QA have failed. The specific commands I'm > running are: > > plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) > print(plmEx) > fit(plmEx, verbose=verbose) > rs <- calculateResiduals(plmTr, verbose=verbose) > ae <- ArrayExplorer(rs) > setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow")) > process(ae, interleaved="auto", verbose=verbose) > > The "process" command runs for a while, but stops after this: > > 20090408 11:26:04| Getting CEL image... > 20090408 11:26:04| Reading CEL image... > num [1:2560, 1:2560] 0 0 0 0 0 0 0 0 0 0 ... > Min. 1st Qu. Median Mean 3rd Qu. Max. > 6.167e-27 7.712e-01 1.005e+00 1.128e+00 1.289e+00 1.338e+02 > 20090408 11:26:08| RAM: 50.0MB > 20090408 11:26:08| Reading CEL image...done > 20090408 11:26:08| Creating Image... > 20090408 11:26:08| Creating Image object from matrix... > 20090408 11:26:08| Rescaling to [0,1]... > Min. 1st Qu. Median Mean 3rd Qu. Max. NA's > 0 Inf Inf Inf Inf Inf 547726 > 20090408 11:26:11| Rescaling to [0,1]...done > 20090408 11:26:13| Interleaving image... > 20090408 11:26:13| Infering horizontal, vertical, or no > interleaving... > Error in z[idxOdd, , ] : incorrect number of dimensions > In addition: Warning message: > In fcn(...) : Packages reordered in search path: package:EBImage > 20090408 11:26:13| Infering horizontal, vertical, or no > interleaving...done > 20090408 11:26:13| Interleaving image...done > 20090408 11:26:13| Creating Image object from matrix...done > 20090408 11:26:13| Color map #1 ('log2,log2neg,rainbow')...done > 20090408 11:26:13| Array #1 of 46 ('O839-A-HuEx-1_0-st-v2-01-1 > (AB-0301)')...done > 20090408 11:26:13|Generating ArrayExplorer report...done > > Here's the output from traceback(): > >> traceback() > 23: mean(x[is.finite(x)]) > 22: safeMeans(abs(z[idxOdd, , ])) > 21: interleave.Image(img, what = interleaved) > 20: interleave(img, what = interleaved) > 19: as.GrayscaleImage.matrix(z, ...) > 18: as.GrayscaleImage(z, ...) > 17: getImage.matrix(y, transforms = transforms, scale = zoom, lim = > zrange, > ..., verbose = less(verbose, 1)) > 16: getImage(y, transforms = transforms, scale = zoom, lim = zrange, > ..., verbose = less(verbose, 1)) > 15: getImage.AffymetrixCelFile(this, ..., verbose = less(verbose), > other = NULL, transforms = list(.Primitive("log2"), function > (x) > { > x <- -x > x[x <= 0] <- NA > log2(x) > }), palette = c("#FF0000FF", "#FF0600FF", "#FF0C00FF", > "#FF1200FF", > ... (elided) ... > "#FF000CFF", "#FF0006FF"), interleaved = "auto", zrange = c > (-15, > 15), transform = .Primitive("log2")) > 14: NextMethod("getImage", this, zrange = zrange, transform = > transform, > palette = palette, ...) > 13: getImage.ResidualFile(this, ..., verbose = less(verbose)) > 12: getImage(this, ..., verbose = less(verbose)) > 11: writeImage.AffymetrixCelFile(df, other = refFile, path = path, > transforms = colorMap$transforms, palette = colorMap$palette, > tags = tags, ..., verbose = less(verbose, 5), interleaved = > "auto") > 10: NextMethod("writeImage", this, ..., tags = tags) > 9: writeImage.ResidualFile(df, other = refFile, path = path, > transforms = colorMap$transforms, > palette = colorMap$palette, tags = tags, ..., verbose = less > (verbose, > 5)) > 8: writeImage(df, other = refFile, path = path, transforms = colorMap > $transforms, > palette = colorMap$palette, tags = tags, ..., verbose = less > (verbose, > 5)) > 7: writeImages.SpatialReporter(reporter, arrays = arrays, aliases = > aliases, > ..., verbose = less(verbose)) > 6: writeImages(reporter, arrays = arrays, aliases = aliases, ..., > verbose = less(verbose)) > 5: FUN(X[[1L]], ...) > 4: lapply.default(reporters, FUN = function(reporter) { > writeImages(reporter, arrays = arrays, aliases = aliases, > ..., verbose = less(verbose)) > }) > 3: lapply(reporters, FUN = function(reporter) { > writeImages(reporter, arrays = arrays, aliases = aliases, > ..., verbose = less(verbose)) > }) > 2: process.ArrayExplorer(ae, interleaved = "auto", verbose = verbose) > 1: process(ae, interleaved = "auto", verbose = verbose) > > and here's the output from sessionInfo(): > >> sessionInfo() > R version 2.9.0 Under development (unstable) (2009-02-22 r47985) > i386-apple-darwin9.6.0 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices datasets utils methods > base > > other attached packages: > [1] abind_1.1-0 preprocessCore_1.5.3 > aroma.affymetrix_1.0.2 > [4] aroma.apd_0.1.3 R.huge_0.1.6 > affxparser_1.15.6 > [7] aroma.core_1.0.2 aroma.light_1.9.2 > EBImage_2.7.21 > [10] digest_0.3.1 matrixStats_0.1.4 > R.rsp_0.3.4 > [13] R.cache_0.1.7 R.utils_1.1.3 > R.oo_1.4.6 > [16] R.methodsS3_1.0.3 > > > Any suggestions? > > -Randy Gobbel > > > > --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. 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