Hi Mike, Did you try to (g)unzip all your CEL files in rawData/GSE15907/MoGene-1_0-st-v1 ?
I don't think that aroma.affymetrix can handle gzipped CEL files. Also, please report your sessionInfo() Best Pierre. On Thu, Jan 28, 2010 at 8:45 AM, mike dewar <[email protected]> wrote: > Hi, > > First of all: apologies if I'm missing something obvious. > > I'm trying to read a set of CEL files from the ImmGen project, > (GSE15907). I'm following the document at > http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis > but I'm running into an error I can't interpret. Any help would be > most appreciated! > > My folder structure is the following: > > /Users/mike/Data/Immgen > |-annotationData > |---chipTypes > |-----MoGene-1_0-st-v1 <--- in here is MoGene-1_0-st-v1,r3.cdf > |---samples > |-rawData > |---GSE15907 > |-----MoGene-1_0-st-v1 <--- in here are lots of gzipped CEL > files > > The code I'm using is > > library('aroma.affymetrix') > setwd("/Users/mike/Data/Immgen") > cdf <- AffymetrixCdfFile$byChipType("MoGene-1_0-st-v1",tags="r3") > cs <- AffymetrixCelSet$byName("GSE15907",cdf=cdf) > print(cs) > > The error I get is > > [2010-01-28 11:41:18] Exception: Argument 'x' is of length 1 although > the range ([0,0]) implies that is should be empty. > at throw(Exception(...)) > at throw.default(sprintf("Argument 'x' is of length %d although the > range ([%s > at throw(sprintf("Argument 'x' is of length %d although the range > ([%s,%s]) im > at getIndices.Arguments(static, ..., length = length) > at getIndices(static, ..., length = length) > at method(static, ...) > at Arguments$getIndex(idx, max = n) > at getFile.GenericDataFileSet(this, 1) > at getFile(this, 1) > at getUnitNamesFile.AffymetrixCelSet(this) > at getUnitNamesFile(this) > at getChipType.AffymetrixCelSet(this) > at getChipType(this) > at sprintf("Chip type: %s", getChipType(this)) > at as.character.AffymetrixCelSet(x) > at as.character(x) > at print(as.character(x)) > at print.Object(cs) > at print(cs) > Calls: print ... getIndices.Arguments -> throw -> throw.default -> > throw -> throw.Exception > Execution halted > > Has anyone got any ideas as to where I'm going wrong? > > Cheers, > > Mike Dewar > > -- > 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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To post to this group, send email to [email protected] > To unsubscribe from this group, send email to > [email protected] > For more options, visit this group at > http://groups.google.com/group/aroma-affymetrix?hl=en > -- 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
