User: Jurat Shahidin
Jurat Shahidin • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- Chicago, IL, USA
- Website:
- https://cs.uic.edu/
- Last seen:
- 11 months, 4 weeks ago
- Joined:
- 5 years, 3 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 18 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 18 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 18 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 18 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 18 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 18 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 19 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 19 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 19 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 19 months ago by
Jurat Shahidin • 80
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