no, On Mon, Oct 10, 2011 at 10:38 AM, rahul <v.rahul.sim...@gmail.com> wrote: > Thanks for the immediate reply. In the affymetrix description of the > CDF file format (http://www.affymetrix.com/support/developer/ > powertools/changelog/gcos-agcc/cdf.html), they have mentioned > 'StartPosition' and 'StopPosition' under "Unit_Block" section. I was > curious if they are of importance. I think they are of not.
My bad then - scrap what I said my I previous message and thanks for the pointer. Either way, the exon pipeline of aroma.affymetrix does not make use of such CDF information. (The only place I could find it is used, is in the bpmapCluster2Cdf() method which is only used when building custom CDFs for tiling arrays). /Henrik > > Thank you, > > Rahul > > On Oct 10, 12:17 pm, Henrik Bengtsson <henrik.bengts...@aroma- > project.org> wrote: >> Hi >> >> >> >> >> >> >> >> >> >> On Mon, Oct 10, 2011 at 9:16 AM, rahul <v.rahul.sim...@gmail.com> wrote: >> > Hello Henrik, >> >> > I am trying to generate a custom CDF file for HuEx-1.0-st-v2, I am >> > having trouble generating the actual StartPosition and StopPosition. >> > Does, Aroma package makes use of these values while processing >> > the .cel files? >> >> > [Unit2315101] >> > Name=NONE >> > Direction=1 >> > NumAtoms=4 >> > NumCells=4 >> > UnitNumber=2315101 >> > UnitType=3 >> > NumberBlocks=1 >> >> > [Unit2315101_Block1] >> > Name=2315101 >> > BlockNumber=1 >> > NumAtoms=4 >> > NumCells=4 >> > StartPosition=3779394 <====== >> > StopPosition=3779397 <====== >> > CellHeader=X Y PROBE FEAT QUAL EXPOS POS CBASE >> > PBASE TBASE ATOM INDEX >> > CODONIND CODON REGIONTYPE REGION >> >> I'm quite sure that 'StartPosition' and 'StopPosition' are *not* part >> of the Affymetrix CDF file format, that is, a CDF file cannot hold >> such extra information. In order words, even if you try to put it in >> a CDF file in text format as above, it will be ignored by an CDF file >> parsers, including the ones converting text CDFs into binary CDFs. >> >> /Henrik >> >> >> >> >> >> >> >> >> >> > Thanks >> >> > Rahul >> >> > On Sep 15, 1:03 pm, rahul <v.rahul.sim...@gmail.com> wrote: >> >> Thanks a lot for the immediate reply. I got your point, I will fix my >> >> CDF and try again. >> >> >> Thank you, >> >> >> Rahul >> >> >> On Sep 15, 12:57 pm, Henrik Bengtsson <henrik.bengts...@aroma- >> >> >> project.org> wrote: >> >> > On Thu, Sep 15, 2011 at 10:49 AM, rahul <v.rahul.sim...@gmail.com> >> >> > wrote: >> >> > > I got the following error, Since i am considering specific probes the >> >> > > number of cells in my CDF file are less compared to the Cel file. Do >> >> > > you know a way to fix the error? >> >> >> > >> setCdf(ds, cdfC); >> >> > > Error in list(`setCdf(ds, cdfC)` = <environment>, >> >> > > `setCdf.AffymetrixCelSet(ds, cdfC)` = <environment>, : >> >> >> > > [2011-09-15 12:41:49] Exception: Cannot set CDF. The specified CDF >> >> > > structure ('HuEx-1_0-st-v2,uniqueprobes') is not compatible with the >> >> > > chip type ('HuEx-1_0-st-v2') of the CEL file. The number of cells do >> >> > > not match: 506944 != 6553600 >> >> >> > A CDF has to specify the same dimension (number of rows and columns of >> >> > probes) as the CEL files, e.g. >> >> >> > > cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2") >> >> > > print(cdf) >> >> >> > AffymetrixCdfFile: >> >> > Path: annotationData/chipTypes/HuEx-1_0-st-v2/ASCII >> >> > Filename: HuEx-1_0-st-v2.cdf >> >> > Filesize: 933.84MB >> >> > File format: v3 (text; ASCII) >> >> > Chip type: HuEx-1_0-st-v2 >> >> > Dimension: 2560x2560 <=== >> >> > Number of cells: 6553600 <=== >> >> > Number of units: 1432154 >> >> > Cells per unit: 4.58 >> >> >> > Here 2560*2560 = 6553600. Your custom CDF has only got 506944 >> >> > (=534*534?) probes. That dimensions are identical is critical, >> >> > because otherwise it is not possible to map probe indices between the >> >> > CEL files and the CDF. >> >> >> > Thus, your custom CDF is not correct. >> >> >> > /Henrik >> >> >> > > at throw(Exception(...)) >> >> > > at throw.default("Cannot set CDF. The specified CDF structure ('", >> >> > > getChipType >> >> > > at throw("Cannot set CDF. The specified CDF structure ('", >> >> > > getChipType(cdf), " >> >> > > at setCdf.AffymetrixCelSet(ds, cdfC) >> >> > > at setCdf(ds, cdfC) >> >> >> > > On Sep 15, 12:35 pm, Henrik Bengtsson <henrik.bengts...@aroma- >> >> > > project.org> wrote: >> >> > >> On Thu, Sep 15, 2011 at 10:29 AM, rahul <v.rahul.sim...@gmail.com> >> >> > >> wrote: >> >> > >> > Thank you for the immediate reply.Yes, It is working fine with the >> >> > >> > regular CDF. I think there is an error in my custom CDF file. I >> >> > >> > will >> >> > >> > look into it. >> >> >> > >> It may help you troubleshoot if you try: >> >> >> > >> chipType <- "HuEx-1_0-st-v2"; >> >> >> > >> cdf <- AffymetrixCdfFile$byChipType(chipType); >> >> > >> print(cdf); >> >> > >> ds <- AffymetrixCelSet$byName("Dataset1", cdf=cdf); >> >> > >> print(ds); >> >> >> > >> cdfC <- AffymetrixCdfFile$byChipType(chipType, tag="uniqueprobes"); >> >> > >> print(cdfC); >> >> > >> setCdf(ds, cdfC); >> >> > >> print(ds); >> >> >> > >> /Henrik >> >> >> > >> > Rahul >> >> >> > >> > On Sep 15, 11:42 am, Henrik Bengtsson <henrik.bengts...@aroma- >> >> > >> > project.org> wrote: >> >> > >> >> Hi, >> >> >> > >> >> On Thu, Sep 15, 2011 at 9:32 AM, rahul <v.rahul.sim...@gmail.com> >> >> > >> >> wrote: >> >> > >> >> > I have generated a custom CDF file. When i try reading the cel >> >> > >> >> > files >> >> > >> >> > using the custom CDF file, I get the following error: >> >> >> > >> >> does it work when you use the default/regular CDF? >> >> >> > >> >> /Henrik >> >> >> > >> >> > Error in list(`AffymetrixCelSet$byName("GBM_TCGA", cdf = cdf)` = >> >> > >> >> > <environment>, : >> >> >> > >> >> > [2011-09-15 10:33:57] Exception: Failed to setup a data set for >> >> > >> >> > any of >> >> > >> >> > 1 data directories located. The following reasons were >> >> > >> >> > reported: (1) >> >> > >> >> > Could not locate a file for this chip type: HuEx-1_0-st-v2 >> >> > >> >> > (while >> >> > >> >> > trying 'rawData/Dataset1/HuEx-1_0-st-v2'). >> >> > >> >> > at throw(Exception(...)) >> >> > >> >> > at throw.default(msg) >> >> > >> >> > at throw(msg) >> >> > >> >> > at method(static, ...) >> >> > >> >> > at AffymetrixCelSet$byName("Dataset1", cdf = cdf) >> >> >> > >> >> > CODE: >> >> >> > >> >> > library(aroma.affymetrix) >> >> > >> >> > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> >> >> > >> >> > chipType <- "HuEx-1_0-st-v2" >> >> > >> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, >> >> > >> >> > tag="uniqueprobes") >> >> > >> >> > cel <- AffymetrixCelSet$byName("Dataset1", cdf=cdf) >> >> >> > >> >> > -- >> >> > >> >> > 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 >> >> > >> >> > websitehttp://www.aroma-project.org/. >> >> > >> >> > To post to this group, send email to >> >> > >> >> > aroma-affymetrix@googlegroups.com >> >> > >> >> > To unsubscribe and other options, go >> >> > >> >> > tohttp://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. >> >> >> > >> > You received this message because you are subscribed to the Google >> >> > >> > Groups "aroma.affymetrix" group with >> >> > >> > websitehttp://www.aroma-project.org/. >> >> > >> > To post to this group, send email to >> >> > >> > aroma-affymetrix@googlegroups.com >> >> > >> > To unsubscribe and other options, go >> >> > >> > tohttp://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. >> >> >> > > You received this message because you are subscribed to the Google >> >> > > Groups "aroma.affymetrix" group with >> >> > > websitehttp://www.aroma-project.org/. >> >> > > To post to this group, send email to aroma-affymetrix@googlegroups.com >> >> > > To unsubscribe and other options, go >> >> > > tohttp://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. >> >> > You received this message because you are subscribed to the Google Groups >> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go tohttp://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. > > > 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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