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.
>
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> >> > --
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> >> > and traceback(), and 3) to post a complete code example.
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> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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>
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--
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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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