User: noorpratap.singh
noorpratap.singh • 280
- Reputation:
- 280
- Status:
- Trusted
- Location:
- University of Maryland
- Website:
- https://github.com/NPSDC
- Last seen:
- 12 hours ago
- Joined:
- 3 years, 4 months ago
- Email:
- n*********@gmail.com
I am in my first year of PhD in Computer Science at University of Maryland.
Posts by noorpratap.singh
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... Are there any remote internship opportunities that are available? ...
written 7 months ago by
noorpratap.singh • 280
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... The folder you mention, does it contain all the files listed by query. To see the total files by query use the following:
`nrow(query$results[[1]])`
Compare with the total downloaded files in your folder.
Further could you send me the exact query you used as it would be then easier to troubleshoo ...
written 7 months ago by
noorpratap.singh • 280
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... In the following command replace "GDCdata" with the local folder name.
`GDCprepare_clinic(query, directory = "GDCdata")` ...
written 7 months ago by
noorpratap.singh • 280
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... Is the option to work remotely available? ...
written 7 months ago by
noorpratap.singh • 280
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... I am not familiar with GEO but data should contain probe level information. The genomic locations of the probes can be extracted from Illumina450K annotation given the data has been retrieved by that.[Illumina Manifest][1]. Once you have that then the [paper][2] outlines a method for associating bet ...
written 8 months ago by
noorpratap.singh • 280
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Comment:
C: Error in GDCprepare
... Updated. Thanks for the advise. ...
written 9 months ago by
noorpratap.singh • 280
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... The following website might help
https://genealacart.genecards.org/Query
You need create an account. In addition directly going to genecards website and typing the RNA in query is also a way around if you have a very limited set of genes
...
written 9 months ago by
noorpratap.singh • 280
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Comment:
C: Error in GDCprepare
... Hi,
Few things.
Coming specifically to your query, the returned object of GDCPrepare is a data.frame (not an object of any other class). Thus you cannot apply assay function. Raw counts are present in the data.frame along with the other elements. To extract them use following:
```
Matrix.C1 <- ...
written 9 months ago by
noorpratap.singh • 280
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Answer:
C: Error in GDCprepare
... Could you please write the query, otherwise its hard to speculate. Further at times errors occur using this package owing to updates. Make sure you update it by typing the following command in R/Rstudio.
```
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
``` ...
written 9 months ago by
noorpratap.singh • 280
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... I have gone through these courses and these actually provide a solid intuition behind the same. ...
written 9 months ago by
noorpratap.singh • 280
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For A: Random forest for gene expression
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