Hi, First of all, I have to say I've got tremendous help from this mailing list, thank you for all of you. Then I have to continue asking for help, I just realize I probably did something very stupid, I was doing DNA copy number segmentation, affymetrix 100k SNP, so as far as I know there are two chips, one chip is obtained by digesting the DNA with Hind, the other chip by Xba.Chip, so in my rawdata folder , I got the .CEL file from both, but in the annotationData folder, sub folder :type, I only got Mapping50K_Hind240,and .cdf file, .ufl, ugp file for hind. My question is, Should I firstly split the .cel file accoding to the chip type and then found the corresponding cdf file etc for Xba.
Many thanks Yan -----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson Sent: 03 December 2010 07:50 To: aroma-affymetrix Subject: Re: [aroma.affymetrix] Help Regarding GCRMA Human Exon. Hi. On Thu, Dec 2, 2010 at 12:08 PM, Prithish Banerjee <prithish.baner...@gmail.com> wrote: > Respected Dr Bengtsson, > I have the following codes and outputs: >> source("http://aroma-project.org/hbLite.R";); >> hbInstall("aroma.affymetrix") I'll assume that you've run this recently so that you have aroma.affymetrix v1.8.0 installed, because then you can do what I explain next. FYI, whenever you get an error, please report what sessionInfo() gives so we can be sure you're up-to-date. Go to the HuEx-1_0-st-v2 chip type page: http://aroma-project.org/chipTypes/HuEx-1_0-st-v2/ and download the Aroma Cell Sequence (ACS) file. Place it in annotationData/chipTypes/HuEx-1_0-st-v2/ (where your CDF is). Don't forget to gunzip. You can drop/move/leave the probe-tab file; it won't be needed anymore. The following script should do: verbose <- Arguments$getVerbose(-10, timestamp=TRUE); dataSet <- "Exon Data"; chipType <- "HuEx-1_0-st-v2"; cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP"); print(cdf); # Assert that the ACS file is available (not really needed to be done) acs <- getAromaCellSequenceFile(cdf); print(acs); # GCRMA background correction bc <- GcRmaBackgroundCorrection(csR, type="affinities"); print(bc); csB <- process(bc, verbose=verbose); print(csB); Finally, I've noticed that you've tried to pass arguments 'cdf' and 'ptf' to process(), i.e. csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose); That is not correct. Was that suggested to you anywhere, or is it just part of your trial-and-error? Let me know if this solves your problem /Henrik >> verbose <- Arguments$getVerbose(-10, timestamp=TRUE); >> dataSet <- "Exon Data" >> chipType <- "HuEx-1_0-st-v2" >> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="fullR3,A20071112,EP") >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/HuEx-1_0-st-v2 > Filename: HuEx-1_0-st-v2,fullR3,A20071112,EP.cdf > Filesize: 203.31MB > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2560x2560 > Number of cells: 6553600 > Number of units: 297051 > Cells per unit: 22.06 > Number of QC units: 1 >> ptf <- AffymetrixProbeTabFile$byChipType(chipType); >> print(ptf) > AffymetrixProbeTabFile: > Name: HuEx-1_0-st-v2 > Tags: > Full name: HuEx-1_0-st-v2 > Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab > File size: 527.80 MB (553438704 bytes) > RAM: 0.01 MB > Number of data rows: NA > Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', 'assembly', > 'seqname', 'start', 'stop', 'strand', 'probeSequence', 'targetStrandedness', > 'category' > Number of text lines: NA > AffymetrixCdfFile: > Path: annotationData/chipTypes/HuEx-1_0-st-v2 > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf > Filesize: 38.25MB > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2560x2560 > Number of cells: 6553600 > Number of units: 18708 > Cells per unit: 350.31 > Number of QC units: 1 >> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType,cdf=cdf) >> print(csR) > AffymetrixCelSet: > Name: Exon Data > Tags: > Path: rawData/Exon Data/HuEx-1_0-st-v2 > Platform: Affymetrix > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP > Number of arrays: 17 > Names: 10_5N, 11_6T, ..., 9_5T > Time period: 2005-05-25 15:34:12 -- 2005-05-26 07:49:40 > Total file size: 1081.22MB > RAM: 0.02MB >> bc <- GcRmaBackgroundCorrection(csR, type="affinities") >> print(bc) > GcRmaBackgroundCorrection: > Data set: Exon Data > Input tags: > User tags: * > Asterisk ('*') tags: GRBC > Output tags: GRBC > Number of files: 17 (1081.22MB) > Platform: Affymetrix > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP > Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm", > indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities", > opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL) > Output path: probeData/Exon Data,GRBC/HuEx-1_0-st-v2 > Is done: FALSE > RAM: 0.00MB >> csB <- process(bc, cdf=cdf, ptf=ptf, verbose=verbose) > 20101202 14:46:02|Background correcting data set... > 20101202 14:46:02| Computing probe affinities (independent of data)... > 20101202 14:46:03| Computing GCRMA probe affinities... > 20101202 14:46:03| Chip type: HuEx-1_0-st-v2 > 20101202 14:46:03| Number of units: 297051 > 20101202 14:46:03| Locating the cell sequence annotation data file... > 20101202 14:46:03| Locating the cell sequence annotation data file...done > 20101202 14:46:03| Computing GCRMA probe affinities...done > 20101202 14:46:03| Computing GCRMA probe affinities... > 20101202 14:46:03| Number of units: 297051 > 20101202 14:46:03| Identify PMs and MMs among the CDF cell indices... > logi [1:5270074] TRUE TRUE TRUE TRUE TRUE TRUE ... > Mode TRUE NA's > logical 5270074 0 > 20101202 14:46:52| MMs are defined as non-PMs > 20101202 14:46:52| Number of PMs: 5270074 > 20101202 14:46:52| Number of MMs: 0 > 20101202 14:46:52| Identify PMs and MMs among the CDF cell indices...done > 20101202 14:46:52| Reading probe-sequence data... > 20101202 14:46:52| Retrieving probe-sequence data... > 20101202 14:46:52| Chip type (full): HuEx-1_0-st-v2,fullR3,A20071112,EP > 20101202 14:46:52| Locating probe-tab file... > 20101202 14:46:52| Chip type: HuEx-1_0-st-v2 > AffymetrixProbeTabFile: > Name: HuEx-1_0-st-v2 > Tags: > Full name: HuEx-1_0-st-v2 > Pathname: > annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab > File size: 527.80 MB (553438704 bytes) > RAM: 0.01 MB > Number of data rows: NA > Columns [12]: 'probeID', 'probeSetID', 'probeXPos', 'probeYPos', > 'assembly', 'seqname', 'start', 'stop', 'strand', 'probeSequence', > 'targetStrandedness', 'category' > Number of text lines: NA > AffymetrixCdfFile: > Path: annotationData/chipTypes/HuEx-1_0-st-v2 > Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf > Filesize: 38.25MB > Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2560x2560 > Number of cells: 6553600 > Number of units: 18708 > Cells per unit: 350.31 > Number of QC units: 1 > 20101202 14:46:52| Locating probe-tab file...done > 20101202 14:46:52| Validating probe-tab file against CDF... > 20101202 14:46:52| Number of records read: 1 > 20101202 14:46:52| Data read: > 'data.frame': 1 obs. of 1 variable: > $ probeSetID: chr "2315101" > - attr(*, "fileHeader")=List of 6 > ..$ comments: NULL > ..$ sep : chr "\t" > ..$ quote : chr "\"" > ..$ skip : num 0 > ..$ topRows :List of 10 > .. ..$ : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ... > .. ..$ : chr "494998" "2315101" "917" "193" ... > .. ..$ : chr "1734213" "2315101" "1092" "677" ... > .. ..$ : chr "4767517" "2315101" "796" "1862" ... > .. ..$ : chr "4286427" "2315101" "986" "1674" ... > .. ..$ : chr "5760145" "2315102" "144" "2250" ... > .. ..$ : chr "671410" "2315102" "689" "262" ... > .. ..$ : chr "4275780" "2315102" "579" "1670" ... > .. ..$ : chr "4293462" "2315102" "341" "1677" ... > .. ..$ : chr "5388" "2315103" "267" "2" ... > ..$ columns : chr "Probe ID" "Probe Set ID" "probe x" "probe y" ... > 20101202 14:46:52| Unit name: > chr "2315101" > 20101202 14:46:55| Unit index: NA > Error in list(`process(bc, cdf = cdf, ptf = ptf, verbose = verbose)` = > <environment>, : > > [2010-12-02 14:46:55] Exception: Failed to identify CDF unit with unit name > '2315101': annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-v2.probe.tab > at throw(Exception(...)) > at throw.default("Failed to identify CDF unit with unit name '", unitNa > at throw("Failed to identify CDF unit with unit name '", unitName, "': > at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose = > at getProbeSequenceData(this, safe = safe, verbose = verbose) > at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver > at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos > at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/ > at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/HuEx-1_0-st-v2", > at do.call("bgAdjustGcrma", args = args) > at process.GcRmaBackgroundCorrection(bc, cdf = cdf, ptf = ptf, verbose > at process(bc, cdf = cdf, ptf = ptf, verbose = verbose) > 20101202 14:46:55| Validating probe-tab file against CDF...done > 20101202 14:46:55| Retrieving probe-sequence data...done > 20101202 14:46:55| Reading probe-sequence data...done > 20101202 14:46:55| Computing GCRMA probe affinities...done > 20101202 14:46:55| Computing probe affinities (independent of data)...done > 20101202 14:46:55|Background correcting data set...done > > Could you please tell me how to rectify the error? > Thank you. > Prithish Banerjee, > Graduate Research Assistant, > Department of Statistics, > West Virginia University. > > -- > 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 with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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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