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 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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