User: Jurat Shahidin
Jurat Shahidin • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- Chicago, IL, USA
- Website:
- https://cs.uic.edu/
- Last seen:
- 4 weeks ago
- Joined:
- 4 years, 4 months ago
- Email:
- j********@gmail.com
I am PhD Student in Artificial Intelligence, Machine learning, Bioinformatics. I am passionate to solve computational problems in bioinformatics in R, Python.
Posts by Jurat Shahidin
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... @Ahill :
Could you provide possible coding demonstration what you were pointing out here? Any possible elaboration? How can I quantify a number of pos/neg correlated features? which posts were you referring to me? Can you specify `how to select a threshold that provides an estimate and bound on the ...
written 7 months ago by
Jurat Shahidin • 80
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... I am working with Affymetric microarray gene expression data for gene filtering. Essentially, I am interested in to extract highly correlated genes by measuring its Pearson correlation, and I got a correlation matrix by doing that. However, for filtering high correlated genes (a.k.a, features), I se ...
written 7 months ago by
Jurat Shahidin • 80
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... yeah, but even simple way of dealing with mixed data by grouping data points and render it a possible 3D plot would be fine. can you have a simple solution for that? Thanks a lot ...
written 7 months ago by
Jurat Shahidin • 80
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... how would you proceed possible PCA and getting 3d scatter plot above pasted data? because can't do PCA for `platform` column, and I need to find out data points that belong to different batch, and two unique platforms in my data. Any possible elaboration? Thanks ...
written 7 months ago by
Jurat Shahidin • 80
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... Hi Jean-Karim Heriche:
Thanks for your heads up. I want to see how data points are similar to each other if we grouped them by different age categories, different batch, and different platform. How can I do that? If I use PCA for the below data, I could get an error. I think I need to have groups ...
written 7 months ago by
Jurat Shahidin • 80
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Any way to clustering mixed data types in microarray data and render them with 3D scatter plot in R?
... Hi all:
I am working with Affymetrix microarray data for my entry to microarray analysis. However, I am trying to see data points distribution within labeled groups in the 3D plot, because I want to see how similar each group of data points in 3D space. To do so, I used `scatterplot3d` package from ...
written 7 months ago by
Jurat Shahidin • 80
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... Dear Kevin:
Thanks for your point. Could you give me a piece of opinion about the way of my above correlation analysis for gene filtering? Do you think what's the decent way for gene filtering here (I used [Affymetrix gene expression data from here][1])? What else I can try for gene filtering? any ...
written 8 months ago by
Jurat Shahidin • 80
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... Dear Kevin:
Thanks for your help. What I want to do is to keep the genes which have a high correlation with `age`. Any correction about what I've done with correlation analysis, indexing, and subsetting original gene expression matrix? your possible instruction would be appreciated a lot. ...
written 8 months ago by
Jurat Shahidin • 80
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... Thanks for your reply. I am experimenting gene expression matrix [public dataset from here][1]. Could you point me out any concrete strategies or approach I could try for gene filtering task? Do you think my way of indexing and subsetting expression matrix is problematic? what's the proper of settin ...
written 8 months ago by
Jurat Shahidin • 80
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... @Kevin Blighe:
Many thanks for your community contribution in Biostars, this thread is very informative and helpful to learn RNA-Seq analysis. ...
written 8 months ago by
Jurat Shahidin • 80
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