User: Monther Alhamdoosh

Reputation:
40
Status:
New User
Location:
Australia/Melbourne/CSL Limited
Twitter:
malhamdoosh
Last seen:
6 months ago
Joined:
2 years, 2 months ago
Email:
m*********@gmail.com

Research Scientist - Bioinformatics 

Posts by Monther Alhamdoosh

<prev • 11 results • page 1 of 2 • next >
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genbankr fails when reading GBK file
... Hi Gabriel,  I was trying to use your package to read a Genbank file but it failed with the following error:  > gb = readGenBank(gbFile, verbose = TRUE) Error in validObject(.Object) : invalid class “GRanges” object: 'mcols(x)' is not parallel to 'x' > traceback() 10: stop(msg, ": ", err ...
genbankr written 6 months ago by Monther Alhamdoosh40 • updated 11 weeks ago by becker.gabriel0
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Answer: A: EGSEA generateReport() error "no adj nodes"
... Hi Jenny,  I just tested the workflow code on Windows and it ran without any errors. You may consider updating your Bioconductor packages to the latest versions before running EGSEA. This could solve the problem.  You can update your packages with library(BiocInstaller) biocLite() Can you pleas ...
written 6 months ago by Monther Alhamdoosh40
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Answer: A: EGSEA generateReport() error "no adj nodes"
... Hi Jenny,  Thanks for raising this issue. Apparently, the error is caused by the topGO package that we use to generate the GO graphs. I just re-run the code on Mac and Linux and it worked without any errors. It seems topGO fails under Windows for the functions we use. I haven't tested that yet. I w ...
written 6 months ago by Monther Alhamdoosh40
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Answer: A: Ensemble EGSEA (EGSEA): base GSA method failures
... Hi Artiz, Thanks for using EGSEA and apologies for the inconvenience error. Can you please post your design and contrast matrices here? And which version of EGSEA are you using? Cheers, Monther On Thu, Apr 13, 2017 at 3:25 AM, irizarnaunk [bioc] < noreply@bioconductor.org> wrote: > Acti ...
written 14 months ago by Monther Alhamdoosh40
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Comment: C: EGSEA usage with microarray data (with vooma)?
... Hi Pekka,  Thank you very much for your valuable feedback! This should help many EGSEA users. I will revisit your suggestions soon and update the package accordingly.  Cheers, Monther  ...
written 16 months ago by Monther Alhamdoosh40
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Comment: C: EGSEA - failing to write report
... Sorry forgot to mention. You should remove brackets as well from the column names. The reason behind is that EGSEA uses the contrast names as part of the file names. So, the contrast name should not have invalid characters. Please try renaming your contrast names following my previous reply.  ...
written 16 months ago by Monther Alhamdoosh40
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Comment: C: EGSEA - failing to write report
... You just need to the remove it from the column names of the contrast matrix as follows colnames(contrasts) = c("contrast1", "contrast2", "contrast3") ...
written 16 months ago by Monther Alhamdoosh40
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Answer: A: EGSEA - failing to write report
... Hi, Please rename your contrasts and remove the "/" character. I think this is the cause of your problem. Cheers, Monther  ...
written 16 months ago by Monther Alhamdoosh40
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Answer: A: EGSEA usage with microarray data (with vooma)?
... Hi Pekka, Thanks for your questions. We do not mention that EGSEA works with microarray datasets since some of the base methods' parameters need to be tuned to suite microarray datasets and we have not tested it with this type of data. We will work on this soon. Let us know if things work well with ...
written 17 months ago by Monther Alhamdoosh40
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Comment: C: EGSEA: how does the program generate the value for the up or down regulation of
... Hi Ying,  No worries! That's right. EGSEA produces p-values that are much smaller than individual methods, particularly for gene sets that are significant in the majority of base methods. Another factor that affects the scale of EGSEA p-values is the individuals methods that are used as some of the ...
written 21 months ago by Monther Alhamdoosh40

Latest awards to Monther Alhamdoosh

Scholar 16 months ago, created an answer that has been accepted. For A: EGSEA - failing to write report
Scholar 16 months ago, created an answer that has been accepted. For A: EGSEA - failing to write report

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