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.
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
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> > 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
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