Determining survival correlation among probes

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Determining survival correlation among probes

Spencer Brackett
Good evening,

 I have a few data objects that are the result of an analysis producing
regression models associated with methylation for TCGA GBM and LGG
subjects. I am trying to figure out how I can use R to find out which
probes among these data objects correlate with patient survival? With this
information, I hope to establish if the gene MGMT is one of the genes whose
methylation show an association with survival. Is there a general procedure
that I might look to as a guide for this? I believe the result of such a
query into probeset data would result in a heatmap visualizing the
association with survival.

Best,

Spencer

        [[alternative HTML version deleted]]

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Re: Determining survival correlation among probes

Bert Gunter-2
Spencer:

Sorry, but I'll be blunt. IMO, you are misusing this list (see the
posting guide). You clearly don't know what you're doing statistically
and need to consult with your advisors. This list cannot and is not
meant to serve that purpose -- it is for for R programming issues. If
your advisors can't or won't help you, you might try
stats.stackexchange.com, which does deal with statistical issues. But
I could not guarantee that they would act as a statistical consulting
service for you, which seems to be what you seek.

Cheers,
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 Fri, Aug 2, 2019 at 8:05 PM Spencer Brackett
<[hidden email]> wrote:

>
> Good evening,
>
>  I have a few data objects that are the result of an analysis producing
> regression models associated with methylation for TCGA GBM and LGG
> subjects. I am trying to figure out how I can use R to find out which
> probes among these data objects correlate with patient survival? With this
> information, I hope to establish if the gene MGMT is one of the genes whose
> methylation show an association with survival. Is there a general procedure
> that I might look to as a guide for this? I believe the result of such a
> query into probeset data would result in a heatmap visualizing the
> association with survival.
>
> 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.

______________________________________________
[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: [FORGED] Re: Determining survival correlation among probes

Rolf Turner

On 3/08/19 3:51 PM, Bert Gunter wrote:

> Spencer:
>
> Sorry, but I'll be blunt. IMO, you are misusing this list (see the
> posting guide). You clearly don't know what you're doing statistically
> and need to consult with your advisors. This list cannot and is not
> meant to serve that purpose -- it is for for R programming issues. If
> your advisors can't or won't help you, you might try
> stats.stackexchange.com, which does deal with statistical issues. But
> I could not guarantee that they would act as a statistical consulting
> service for you, which seems to be what you seek.

I very firmly agree with Bert's post.  It seems to me that Spencer's
postings demonstrate fundamental misunderstanding both of R and of
statistical science.  He gives the impression that he *thinks* he
understands a great deal more than he actually does, with the result
that the questions he asks are generally ill-conceived and ill-posed.
He appears to be attempting advanced statistical analysis without having
mastered the elementary basics.

Spencer should focus on remedying his misconceptions and filling in the
lacunae in his knowledge.

cheers,

Rolf Turner

--
Honorary Research Fellow
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

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and provide commented, minimal, self-contained, reproducible code.