I'm having difficulty finding a reasonable way to format the
annotation
data that Affymetrix provides (both MAGE-ML XML and a similar CSV
file)
into a BioC annotation package.
I've read the AnnBuilder vignette and it seems to assume that one
starts with a format other than what Affy provides. I've also read
that the RMAGE-ML package can take the Affy MAGE-ML package and format
it for use within limma, and a few other packages, but affy (or
annaffy
or AnnBuilder) isn't listed as one of them.
Can anyone help me out as to what method would be most efficient for
formatting this MAGE-ML file into a format acceptable for use within
BioC as a general annotation file? I can't find any such packages
currently available for the Yeast 2.0 chip.
Thanks in advance,
Jake Michaelson
> I'm having difficulty finding a reasonable way to format the
annotation
> data that Affymetrix provides (both MAGE-ML XML and a similar CSV
file)
> into a BioC annotation package.
>
> I've read the AnnBuilder vignette and it seems to assume that one
> starts with a format other than what Affy provides. I've also read
> that the RMAGE-ML package can take the Affy MAGE-ML package and
format
> it for use within limma, and a few other packages, but affy (or
annaffy
> or AnnBuilder) isn't listed as one of them.
RMAGEML is currently devoted to conversion from MAGE-ML archives
of experiment results to marray type data structures in R. I
understand
that this functionality will be expanded in the direction of affy
archives, but I am not sure it will address the use of MAGE-ML
for creation of platform annotation environments.
>
> Can anyone help me out as to what method would be most efficient for
> formatting this MAGE-ML file into a format acceptable for use within
> BioC as a general annotation file? I can't find any such packages
> currently available for the Yeast 2.0 chip.
I will look at the MAGE-ML serialization and see if it is
easy to come up with something using the XML library. But it
may well be easier to work from the CSV.
AnnBuilder would clearly be the tool of choice for this activity,
but I don't believe it can transform directly from an Affx annot CSV
to the desired set of environments. We can improvise something
fairly simply; I recently did it for zebrafish, but the results do
not emulate exactly the structures in the other affy chip annotation
packages.
I will post some partial solutions in a few moments. There are
various ways of getting something useful, and the path taken
will depend upon the ultimate requirements. If we want to be sure
that something like annaffy will behave well with the target platform,
we may have more stringent requirements than if we are just interested
in doing manual lookups.
What is the current level of support in Bioconductor
for the binary Affy GCOS formats?
Is there a current best practice for converting from
TEXT to BINARY and vice versa?
[ Sorry if this is a repeat question, I got the mail
dumps for last few months and greped around in it but
could find little ]
Richard Finney wrote:
> What is the current level of support in Bioconductor
> for the binary Affy GCOS formats?
Currently the binary .cel files are supported. Support for binary .cdf
files should exist very soon. For the average end user, the binary
.cdf
support should be a moot point, as the affy package automagically
downloads and installs required cdfenvs. All but five or six of the
existing .cdf files are downloadable from the BioC website, and as
soon
as we have support for the binary .cdfs they will all be available.
>
> Is there a current best practice for converting from
> TEXT to BINARY and vice versa?
>
> [ Sorry if this is a repeat question, I got the mail
> dumps for last few months and greped around in it but
> could find little ]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
I have created a custom CDF file.
The purpose is to measure the expression of splice
variations.
I place the file in the same directory as the CEL
files and crank up R and do the usual BIOC
incantation.
Based on a suggestion offered by the brainiacs at
University of Michigan (
http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/cdf
readme.htm#How_to_use_the_custom_CDF_file:_
)
I try something like this ...
data<-ReadAffy();
data@cdfName<-"NEW.CDF"
But subsequent data processing calls attempt to
connect to the internet and get a CDF file from there.
Obviously, I missing something.
Anybody got any ideas?
Please add to any "RTFM" responses a specific FM to
read.
Thanks!
Rich
I think that you need to hand edit the cel files and put the name of
your new custom CDF env in there. Since that is where the software
looks to decide what CDF it needs.
Robert
On Jan 25, 2005, at 8:04 PM, Richard Finney wrote:
>
> I have created a custom CDF file.
>
> The purpose is to measure the expression of splice
> variations.
>
> I place the file in the same directory as the CEL
> files and crank up R and do the usual BIOC
> incantation.
>
> Based on a suggestion offered by the brainiacs at
> University of Michigan (
> http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/
> cdfreadme.htm#How_to_use_the_custom_CDF_file:_
> )
> I try something like this ...
>
> data<-ReadAffy();
> data@cdfName<-"NEW.CDF"
>
> But subsequent data processing calls attempt to
> connect to the internet and get a CDF file from there.
>
> Obviously, I missing something.
>
> Anybody got any ideas?
>
> Please add to any "RTFM" responses a specific FM to
> read.
>
> Thanks!
>
> Rich
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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