Re: [aroma.affymetrix] Is it necessary to update annotation files (CytoscanHD array)

[Chengyu Liu]

Thanks very much, Henrik。Then I will not update these files. I will use the 
ones you provided. Now I am trying to get the pipeline working. 



On Monday, January 12, 2015 at 11:47:17 PM UTC+2, Henrik Bengtsson wrote:
>
> Hi. 
>
> The Aroma Cell Sequence (ACS) file does not have to be updated, since 
> it only contains the probe sequences on the array and those never 
> changes. 
>
> The Unit Genome Position (UGP) file specifies the (chr, pos) genomic 
> coordinates for the probe sets, which depends on the genome 
> reference/build.  Likewise, the Unit Fragment Length (UFL) file 
> specify the PCR fragment lengths as cut by the restriction enzyme 
> (part of the Affymetrix assay).  These cut locations also depend on 
> the genome reference/build.  So, yes, UGP and UFL files needs to match 
> the genome build wanted.  (However, I wouldn't expect much any 
> major/noticeable difference in CN estimates if not perfect version 
> matching since not too much have changed and most discrepancies would 
> come through as a few number outliers). 
>
> To build newer versions yourself, please see how-to docs: 
>
> * Create a Unit Genome Position (UGP) files 
> * Create a Unit Fragment Length (UFL) files 
>
> available via http://aroma-project.org/howtos/ 
> 
>  
>
> Hope this helps 
>
> Henrik 
>
>
> On Thu, Jan 8, 2015 at 5:44 AM, Chengyu Liu  > wrote: 
> > Hi, 
> > 
> > Is it necessary to update annotation files in 
> > 
> http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/. 
>
> > It is quite old. Or I can use them without update. 
> > 
> > Br, 
> > C.Y 
> > 
> > -- 
> > -- 
> > 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. 
> > 
> > 
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>  
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] Is it necessary to update annotation files (CytoscanHD array)

[Henrik Bengtsson]

Hi.

The Aroma Cell Sequence (ACS) file does not have to be updated, since
it only contains the probe sequences on the array and those never
changes.

The Unit Genome Position (UGP) file specifies the (chr, pos) genomic
coordinates for the probe sets, which depends on the genome
reference/build.  Likewise, the Unit Fragment Length (UFL) file
specify the PCR fragment lengths as cut by the restriction enzyme
(part of the Affymetrix assay).  These cut locations also depend on
the genome reference/build.  So, yes, UGP and UFL files needs to match
the genome build wanted.  (However, I wouldn't expect much any
major/noticeable difference in CN estimates if not perfect version
matching since not too much have changed and most discrepancies would
come through as a few number outliers).

To build newer versions yourself, please see how-to docs:

* Create a Unit Genome Position (UGP) files
* Create a Unit Fragment Length (UFL) files

available via http://aroma-project.org/howtos/

Hope this helps

Henrik


On Thu, Jan 8, 2015 at 5:44 AM, Chengyu Liu  wrote:
> Hi,
>
> Is it necessary to update annotation files in
> http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/.
> It is quite old. Or I can use them without update.
>
> Br,
> C.Y
>
> --
> --
> 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/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.

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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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[aroma.affymetrix] Is it necessary to update annotation files (CytoscanHD array)

[Chengyu Liu]

Hi,

Is it necessary to update annotation files 
in 
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/. 
It is quite old. Or I can use them without update.

Br,
C.Y

-- 
-- 
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.


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