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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>>
>> > --
>> > 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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>
--
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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