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
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
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> > >> >> > 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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> > >> > 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
"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/
