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
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>> > >> >> > 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/
>
--
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/
