Sorry, changed network points and reposted by accident. Thanks for your help. This should be enough to get me thinking for a bit.
On Feb 3, 2009, at 3:23 PM, Henrik Bengtsson wrote: > > Ok, sorry I didn't answer you question explicitly. No, they do not > have to contain ChrX and ChrY data. However, but independent of your > question, I would recommend that you import all annotation data > available, since that might become of interest in future usage. > > Currently part of the code is hardwired to assume the human genome. > Thus, if you pass "-XY", it interprets "X" to correspond to chromosome > 23 and "Y" to be chromosome 24. So, '-XY' tries to exclude units on > chromosome 23 and 24. The plan is to support genome specific > annotation data where you can specify what chromosome index "X" and > "Y" maps to. The directory annotationData/genomes/ is reserved for > this, and the ChromosomeExplorer is somewhat sensitive to this. But > that is all future plans. > > /Henrik > > On Tue, Feb 3, 2009 at 1:03 PM, David Rosenberg > <[email protected]> wrote: >> >> Do they ufl/ugp/acc files need to be build with X and Y chromosomes >> included? If so, this won't be too hard to fix. >> >> >> On Jan 30, 9:50 pm, David Rosenberg <[email protected]> >> wrote: >>> As I think about this further, it occurs to me that there are other >>> potential problems with this chip/cdf. I was looking at the ugp/ufl >>> files and it appears that fragment length normalization etc. is >>> performed on a unit-by-unit basis. The way the array/cdf is >>> currently >>> structured, not all probes in a particular unit are precisely co- >>> located. While the location differences within a unit are quite >>> small >>> (100 bp or so), this does result in units where probes hybridize to >>> multiple digestion fragments. This definitely 'breaks' fragment >>> length normalization as I see it currently implemented. Now, the >>> cdf >>> can be restructured such that all units map to a single genomic >>> location, but that seems to preclude merging/summarizing further >>> down >>> the analysis workflow. If there were a way to perform these >>> normalization procedures on a per-probe basis rather than a per-unit >>> basis, this would be preferable. Let me know your thoughts. >>> >>> On Jan 30, 2009, at 6:41 PM, Henrik Bengtsson wrote: >>> >>> >>> >>>> Hi, >>> >>>> could you please forward your UGP file to me; I think I know what >>>> the >>>> problem is, but I guess it easier for me to check it myself first. >>> >>>> BTW, although this looks like a custom CDF - if you want to, I >>>> can put >>>> up a group page specific to this chip type, documenting the chip >>>> type >>>> (and either link or host those annotation files). Might be useful >>>> for >>>> a future fellow researcher. It's your call. >>> >>>> /Henrik >>> >>>> On Fri, Jan 30, 2009 at 12:08 PM, David Rosenberg >>>> <[email protected]> wrote: >>> >>>>> I am receiving the following errors when attempting to perform >>>>> allelic >>>>> crosstalk calibration on a dataset using a custom CDF. I don't >>>>> know >>>>> if this is indicative of errors in the internal structure of the >>>>> CDF, >>>>> or if there are parameters that I must pass to >>>>> AllelicCrosstalkCalibration due to the properties of the CDF >>>>> (i.e. # >>>>> of chromosomes, etc.) >>> >>>>>> library("aroma.affymetrix") >>>>> Loading required package: R.utils >>>>> Loading required package: R.oo >>>>> Loading required package: R.methodsS3 >>>>> R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ? >>>>> R.methodsS3 >>>>> for help. >>>>> R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help. >>>>> R.utils v1.1.3 (2009-01-12) successfully loaded. See ?R.utils for >>>>> help. >>>>> Loading required package: aroma.core >>>>> Loading required package: R.cache >>>>> R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for >>>>> help. >>>>> Loading required package: R.rsp >>>>> R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for >>>>> help. >>>>> Type browseRsp() to open the RSP main menu in your browser. >>>>> Loading required package: matrixStats >>>>> Loading required package: digest >>>>> Loading required package: aroma.light >>>>> aroma.light v1.11.1 (2009-01-12) successfully loaded. See ? >>>>> aroma.light >>>>> for help. >>>>> aroma.core v1.0.0 (2009-01-12) successfully loaded. See ? >>>>> aroma.core >>>>> for help. >>>>> Loading required package: affxparser >>>>> Loading required package: R.huge >>>>> R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for >>>>> help. >>>>> Loading required package: aroma.apd >>>>> aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ? >>>>> aroma.apd for >>>>> help. >>>>> aroma.affymetrix v1.0.0 (2009-01-12) successfully loaded. See ? >>>>> aroma.affymetrix for help. >>> >>>>>> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >>> >>>>>> # Don't display too many decimals. >>>>>> options(digits=4) >>>>>> chipType="MOUSEDIVm520650" >>>>>> cdf<-AffymetrixCdfFile$byChipType("MOUSEDIVm520650") >>>>>> print(cdf) >>>>> AffymetrixCdfFile: >>>>> Path: annotationData/chipTypes/MOUSEDIVm520650 >>>>> Filename: MOUSEDIVm520650.CDF >>>>> Filesize: 463.91MB >>>>> Chip type: MOUSEDIVm520650 >>>>> RAM: 0.00MB >>>>> File format: v4 (binary; XDA) >>>>> Dimension: 2572x2680 >>>>> Number of cells: 6892960 >>>>> Number of units: 973990 >>>>> Cells per unit: 7.08 >>>>> Number of QC units: 4 >>>>>> gi<-getGenomeInformation(cdf) >>>>>> print(gi) >>>>> UgpGenomeInformation: >>>>> Name: MOUSEDIVm520650 >>>>> Tags: DMR20090129 >>>>> Pathname: annotationData/chipTypes/MOUSEDIVm520650/ >>>>> MOUSEDIVm520650,DMR20090129.ugp >>>>> File size: 4.64MB >>>>> RAM: 0.00MB >>>>> Chip type: MOUSEDIVm520650 >>>>>> si<-getSnpInformation(cdf) >>>>>> print(si) >>>>> UflSnpInformation: >>>>> Name: MOUSEDIVm520650 >>>>> Tags: DMR20090129 >>>>> Pathname: annotationData/chipTypes/MOUSEDIVm520650/ >>>>> MOUSEDIVm520650,DMR20090129.ufl >>>>> File size: 3.72MB >>>>> RAM: 0.00MB >>>>> Chip type: MOUSEDIVm520650 >>>>> Number of enzymes: 2 >>>>>> acs<-AromaCellSequenceFile$byChipType(getChipType(cdf, >>>>>> fullname=FALSE)) >>>>>> print(acs) >>>>> AromaCellSequenceFile: >>>>> Name: MOUSEDIVm520650 >>>>> Tags: DMR20090129 >>>>> Pathname: annotationData/chipTypes/MOUSEDIVm520650/ >>>>> MOUSEDIVm520650,DMR20090129.acs >>>>> File size: 170.91MB >>>>> RAM: 0.00MB >>>>> Number of data rows: 6892960 >>>>> File format: v1 >>>>> Dimensions: 6892960x26 >>>>> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, >>>>> raw, >>>>> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, >>>>> raw, >>>>> raw >>>>> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, >>>>> 1, 1, >>>>> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 >>>>> Footer: <createdOn>20090129 12:45:11 CST</ >>>>> createdOn><platform>Affymetrix</ >>>>> platform><chipType>MOUSEDIVm520650</ >>>>> chipType> >>>>> Chip type: MOUSEDIVm520650 >>>>> Platform: Affymetrix >>>>>> csR<-AffymetrixCelSet$byName("mDIV/testset", cdf=cdf) >>>>>> print(csR) >>>>> AffymetrixCelSet: >>>>> Name: testset >>>>> Tags: >>>>> Path: rawData/mDIV/testset/MOUSEDIVm520650 >>>>> Platform: Affymetrix >>>>> Chip type: MOUSEDIVm520650 >>>>> Number of arrays: 44 >>>>> Names: SNP_mDIV_A10-10_081308, SNP_mDIV_A10-201_091708, ..., >>>>> SNP_mDIV_A9-9_081308 >>>>> Time period: 2008-08-13 15:39:47 -- 2008-09-18 00:20:33 >>>>> Total file size: 2899.65MB >>>>> RAM: 0.06MB >>>>> There were 50 or more warnings (use warnings() to see the first >>>>> 50) >>>>>> acc<-AllelicCrosstalkCalibration(csR, model="CRMAv2") >>>>>> print(acc) >>>>> AllelicCrosstalkCalibration: >>>>> Data set: testset >>>>> Input tags: >>>>> User tags: * >>>>> Asterisk ('*') tags: ACC,ra,-XY >>>>> Output tags: ACC,ra,-XY >>>>> Number of files: 44 (2899.65MB) >>>>> Platform: Affymetrix >>>>> Chip type: MOUSEDIVm520650 >>>>> Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200, >>>>> subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, >>>>> flavor: chr >>>>> "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 >>>>> 0.075 >>>>> 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98) >>>>> Output path: probeData/testset,ACC,ra,-XY/MOUSEDIVm520650 >>>>> Is done: FALSE >>>>> RAM: 0.01MB >>>>>> csC<-process(acc, verbose=verbose) >>>>> 20090130 14:03:43|Calibrating data set for allelic cross talk... >>>>> Error in if (any(units < 1)) stop("Argument 'units' contains non- >>>>> positive indices.") : >>>>> missing value where TRUE/FALSE needed >>>>> 20090130 14:03:43|Calibrating data set for allelic cross >>>>> talk...done >>>>>> traceback() >>>>> 13: readCdfCellIndices(pathname, ...) >>>>> 12: getCellIndicesChunk(getPathname(this), units = >>>>> unitsChunk, ..., >>>>> verbose = verbose) >>>>> 11: fcn(idxs[ii], ...) >>>>> 10: lapplyInChunks.numeric(units, function(unitsChunk) { >>>>> cdfChunk <- getCellIndicesChunk(getPathname(this), units = >>>>> unitsChunk, >>>>> ..., verbose = verbose) >>>>> res <- vector("list", length(unitsChunk)) >>>>> res[[1]] <- unlist(cdfChunk, use.names = useNames) >>>>> res >>>>> }, chunkSize = 1e+05, useNames = useNames, verbose = verbose) >>>>> 9: lapplyInChunks(units, function(unitsChunk) { >>>>> cdfChunk <- getCellIndicesChunk(getPathname(this), units = >>>>> unitsChunk, >>>>> ..., verbose = verbose) >>>>> res <- vector("list", length(unitsChunk)) >>>>> res[[1]] <- unlist(cdfChunk, use.names = useNames) >>>>> res >>>>> }, chunkSize = 1e+05, useNames = useNames, verbose = verbose) >>>>> 8: getCellIndices.AffymetrixCdfFile(cdf, units = subset, >>>>> useNames = >>>>> FALSE, >>>>> unlist = TRUE) >>>>> 7: getCellIndices(cdf, units = subset, useNames = FALSE, unlist = >>>>> TRUE) >>>>> 6: getSubsetToAvg.AllelicCrosstalkCalibration(this) >>>>> 5: getSubsetToAvg(this) >>>>> 4: getParameters.AllelicCrosstalkCalibration(this) >>>>> 3: getParameters(this) >>>>> 2: process.AllelicCrosstalkCalibration(acc, verbose = verbose) >>>>> 1: process(acc, verbose = verbose) >>> >> > > > --~--~---------~--~----~------------~-------~--~----~ 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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