User: Jurat Shahidin

Reputation:
80
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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

<prev • 83 results • page 1 of 9 • next >
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Comment: C: How to quantify positive and negative correlated genes from gene expression data
... @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 Shahidin80
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How to quantify positive and negative correlated genes from gene expression data?
... 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 ...
gene R correlation gene-expression filtering written 7 months ago by Jurat Shahidin80
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Comment: C: Any way to clustering mixed data types in microarray data and render them with 3
... 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 Shahidin80
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Comment: C: Any way to clustering mixed data types in microarray data and render them with 3
... 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 Shahidin80
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Comment: C: Any way to clustering mixed data types in microarray data and render them with 3
... 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 Shahidin80
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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 ...
scatter-plot R microarray clustering written 7 months ago by Jurat Shahidin80
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Comment: C: what is the strategy to set threshold value for filtering gene expression matrix
... 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 Shahidin80
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Comment: C: what is the strategy to set threshold value for filtering gene expression matrix
... 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 Shahidin80
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Comment: C: what is the strategy to set threshold value for filtering gene expression matrix
... 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 Shahidin80
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Comment: C: Survival analysis with gene expression
... @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 Shahidin80

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