Accessing/Visualizing Probe Sets to determine Data Association

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Accessing/Visualizing Probe Sets to determine Data Association

Spencer Brackett
 Good evening,

  I am dealing with an already analyzed  .RData file consisting of
pre-configured data objects loaded into my environment. I am attempting to
take this data, which shows an overall correlation of survival with
methylation pattern for a form of brain cancer, and go to the individual
probe sets and see if MGMT is one of the genes whose methylation show an
association with survival. To do this I am under the impression that I have
to visualize the probesets in order to view them/determine what gene or
genes (unbiasedly) show an association between meth. and survival. I have
been trying to run a few different methods such as microarray probe set
mapping through Ensembl, but without avail.
Would anyone perhaps know of a procedure/workflow that I could use to
achieve this?

Best,

Spencer

        [[alternative HTML version deleted]]

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Re: Accessing/Visualizing Probe Sets to determine Data Association

Bert Gunter-2
This query should almost certainly be posted on the Bioconductor Help site
rather than here. Especially so as it is a general question about a
genomics "workflow" rather than a question about R programming.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Jul 18, 2019 at 12:55 PM Spencer Brackett <
[hidden email]> wrote:

>  Good evening,
>
>   I am dealing with an already analyzed  .RData file consisting of
> pre-configured data objects loaded into my environment. I am attempting to
> take this data, which shows an overall correlation of survival with
> methylation pattern for a form of brain cancer, and go to the individual
> probe sets and see if MGMT is one of the genes whose methylation show an
> association with survival. To do this I am under the impression that I have
> to visualize the probesets in order to view them/determine what gene or
> genes (unbiasedly) show an association between meth. and survival. I have
> been trying to run a few different methods such as microarray probe set
> mapping through Ensembl, but without avail.
> Would anyone perhaps know of a procedure/workflow that I could use to
> achieve this?
>
> Best,
>
> Spencer
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Accessing/Visualizing Probe Sets to determine Data Association

Spencer Brackett
My apologies

On Thu, Jul 18, 2019 at 4:00 PM Bert Gunter <[hidden email]> wrote:

> This query should almost certainly be posted on the Bioconductor Help site
> rather than here. Especially so as it is a general question about a
> genomics "workflow" rather than a question about R programming.
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Thu, Jul 18, 2019 at 12:55 PM Spencer Brackett <
> [hidden email]> wrote:
>
>>  Good evening,
>>
>>   I am dealing with an already analyzed  .RData file consisting of
>> pre-configured data objects loaded into my environment. I am attempting to
>> take this data, which shows an overall correlation of survival with
>> methylation pattern for a form of brain cancer, and go to the individual
>> probe sets and see if MGMT is one of the genes whose methylation show an
>> association with survival. To do this I am under the impression that I
>> have
>> to visualize the probesets in order to view them/determine what gene or
>> genes (unbiasedly) show an association between meth. and survival. I have
>> been trying to run a few different methods such as microarray probe set
>> mapping through Ensembl, but without avail.
>> Would anyone perhaps know of a procedure/workflow that I could use to
>> achieve this?
>>
>> Best,
>>
>> Spencer
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.