Admin: Marcel Ramos
Marcel Ramos ♦♦ 140
- Reputation:
- 140
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 5 days, 21 hours ago
- Joined:
- 3 years, 4 months ago
- Email:
- m***********@roswellpark.org
Posts by Marcel Ramos
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... Hi Benjamin,
It would be good to have Tiago Silva's input on this.
It seems like, at least for this case, the curation process considered the TNM stages
and coded for Stage IV
Here are a few other resources that you can use to check these variables
(many of which yield NA for pathologic_stage):
Geno ...
written 5 weeks ago by
Marcel Ramos ♦♦ 140
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... Hi Ankita,
I was unable to reproduce the error. I suspect that it may have something to do with your internet connection.
Please check your connection settings and make sure that a firewall or VPN is not preventing you from
accessing the remote file.
There are other known issues for users of Wi ...
written 10 weeks ago by
Marcel Ramos ♦♦ 140
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... Hi Melissa,
Without a reproducible example, there is not much specific help that fellow Bioconductor users can provide.
If you have the ranges of those variants that have been merged, you can use findOverlaps to find the overlapping ranges in the original GRanges that correspond to those variant acc ...
written 10 weeks ago by
Marcel Ramos ♦♦ 140
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222
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... Hi Lloyd,
Thanks for posting a solution!
Best regards,
Marcel
...
written 12 weeks ago by
Marcel Ramos ♦♦ 140
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... Hi Mario,
Thank you for posting on the support site.
Yes, there is a method to add an experiment using the c function.
This works quite easily if this experiment has the same sample composition and
order as another experiment. You can then use:
c(mymultiassay, newExpAssay = tcia, mapFrom = 1L)
Ot ...
written 3 months ago by
Marcel Ramos ♦♦ 140
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... Hi znl207,
In order for anyone to provide assistance, please post a fully reproducible and
minimal example of the issue.
What I see from the output, it doesn't look like an error but more of a warning.
It could be related to a number of issues including the integrity of the data.
One option you coul ...
written 4 months ago by
Marcel Ramos ♦♦ 140
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... Hi Carlos,
Thank you for your report. This is indeed a bug in the subsetByOverlaps,RaggedExperiment,Vector-method.
This was fixed in version 1.2.4 in release and 1.3.7 in devel.
Regards,
Marcel
...
written 6 months ago by
Marcel Ramos ♦♦ 140
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... Hi Michael Wang,
This seems to be a memory issue.
Methylation data is quite large and may exhaust your memory resources when trying
to merge the various files that you've downloaded.
The total size of the files is ~10.8 Gb.
Downloading data for project TCGA-LUAD
GDCdownload will download 507 files ...
written 6 months ago by
Marcel Ramos ♦♦ 140
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... Updates: This has been fixed in `1.2.3` in release and `1.3.5` in devel.
Marcel
...
written 6 months ago by
Marcel Ramos ♦♦ 140
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283
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... Hi Taran,
Apologies for the late response. I have looked at the issue and we're working on a fix.
The reason you're getting an error in that call is that you are introducing an "score" column
of type `factor`.
The quick fix for this issue is to coerce the "score" column to character and rerun th ...
written 6 months ago by
Marcel Ramos ♦♦ 140
Latest awards to Marcel Ramos
Scholar
12 months ago,
created an answer that has been accepted.
For A: Classes and methods for working with segmented copy number data
Scholar
14 months ago,
created an answer that has been accepted.
For A: Classes and methods for working with segmented copy number data
Scholar
14 months ago,
created an answer that has been accepted.
For A: Classes and methods for working with segmented copy number data
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