User: Monther Alhamdoosh

Reputation:
40
Status:
New User
Location:
Australia/Melbourne/CSL Limited
Twitter:
malhamdoosh
Last seen:
9 months, 1 week ago
Joined:
1 year, 8 months ago
Email:
m*********@gmail.com

Research Scientist - Bioinformatics 

Posts by Monther Alhamdoosh

<prev • 8 results • page 1 of 1 • next >
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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 7 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 9 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 9 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 9 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 9 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 10 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 14 months ago by Monther Alhamdoosh40
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Answer: A: EGSEA: how does the program generate the value for the up or down regulation of
... Hi Ying,  Thanks for trying out our package! The Direction column in EGSEA is calculated based on the logFC values that are calculated using limma::topTable (if it was not provided). We simply count the number of genes that are up- and down-regulated in the gene set and make a decision based on the ...
written 14 months ago by Monther Alhamdoosh40

Latest awards to Monther Alhamdoosh

Scholar 9 months ago, created an answer that has been accepted. For A: EGSEA - failing to write report
Scholar 9 months ago, created an answer that has been accepted. For A: EGSEA - failing to write report

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