no, On Mon, Oct 10, 2011 at 10:38 AM, rahul <v.rahul.sim...@gmail.com> wrote:
> Thanks for the immediate reply. In the affymetrix description of the
> CDF file format (http://www.affymetrix.com/support/developer/
> powertools/changelog/gcos-agcc/cdf.html), they have mentioned
> 'StartPosition' and 'StopPosition' under "Unit_Block" section. I was
> curious if they are of importance. I think they are of not.
My bad then - scrap what I said my I previous message and thanks for
the pointer. Either way, the exon pipeline of aroma.affymetrix does
not make use of such CDF information. (The only place I could find it
is used, is in the bpmapCluster2Cdf() method which is only used when
building custom CDFs for tiling arrays).
/Henrik
>
> Thank you,
>
> Rahul
>
> On Oct 10, 12:17 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> 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 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
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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/.
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