Problem loading hg19 refGene/fefFlat file

[joshua_l]

Hi Cheng,

I'm using the 64-bit dChip version, Build date: Apr 13 2010. When
performing CNV analysis, I'm having problems loading the refGene or
refFlat file for hg19 downloaded from UCSC Genome Bioinformatics
Sequence and Annotation Downloads. When dChip tries to load the file,
an error message "MAX_REFGENE_NUM limit reached" appears and my
analysis is stopped. The maximum number for dChip seems to be 29,600
while the hg19 file has 40,901 entries.

I would like to know if you have an edited version of the hg19 refFlat/
refGene file for dChip, or is there a newer version which can handle
the larger number of gene entries.

Thank you and hope to hear from you soon.

Regards,
Joshua

[Cheng Li]

Joshua,

Thank you for the notice. Please use this updated version:
https://www.sugarsync.com/pf/D7557330_1066077_60866

Cheng

http://www.ChengLiLab.org/

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[joshua_l]

Hi Cheng,

Thank you for the updated version, and loading the refGene/refFlat
file is fine. However, when I try to switch between data types, an
error message "NumSigRegion >= MAX_SIG_REGION" will always appear. I'm
still able to click on the chromsome branch on the left panel, and
view the different data types, but I'm not sure if there's any display
error, as I've not looked into it in detail.

Do hope to hear from you regarding this issue. Thank you once again.

Regards,
Joshua

On Nov 18, 12:22 pm, Cheng Li <lch3...@gmail.com> wrote:
> Joshua,
>
> Thank you for the notice. Please use this updated version:https://www.sugarsync.com/pf/D7557330_1066077_60866
>

> Chenghttp://www.ChengLiLab.org/

>
>
>
> On Thu, Nov 17, 2011 at 7:16 PM, joshua_l <lysjos...@gmail.com> wrote:
> > Hi Cheng,
>
> > I'm using the 64-bit dChip version, Build date: Apr 13 2010. When
> > performing CNV analysis, I'm having problems loading the refGene or
> > refFlat file for hg19 downloaded from UCSC Genome Bioinformatics
> > Sequence and Annotation Downloads. When dChip tries to load the file,
> > an error message "MAX_REFGENE_NUM limit reached" appears and my
> > analysis is stopped. The maximum number for dChip seems to be 29,600
> > while the hg19 file has 40,901 entries.
>
> > I would like to know if you have an edited version of the hg19 refFlat/
> > refGene file for dChip, or is there a newer version which can handle
> > the larger number of gene entries.
>
> > Thank you and hope to hear from you soon.
>
> > Regards,
> > Joshua
>
> > --
> > This message is from the dChip Software user group.
> > -- If you ask dChip questions, please include dChip output messages,
> > generated files, or screenshots to help rapid debugging.
> > -- To post to this group, send email to dchip-s...@googlegroups.com
> > -- To unsubscribe from this group, send email to
> > dchip-softwar...@googlegroups.com
> > -- For the latest updates or to change email options, visit this group at

> >http://groups.google.com/group/dchip-software- Hide quoted text -
>
> - Show quoted text -