Thanks for the clarification. Rahul
On Oct 10, 1:53 pm, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > 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 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/
