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
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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>
> > --
> > 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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--
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
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