User: Jurat Shahidin

Reputation:
60
Status:
Trusted
Location:
Chicago, IL, USA
Website:
https://cs.uic.edu/
Last seen:
21 minutes ago
Joined:
3 years, 8 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 • 62 results • page 1 of 7 • next >
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... thanks for your reply. I got this error after I remove `0+`: > row dimension of design doesn't match column dimension of data object why is that? how can I cut down `exprs_mat` with the shortlist of genes? ...
written 1 hour ago by Jurat Shahidin60
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... > Your topTable() should have the genes that correlate nicely to $GA I am trying to get these nicely correlated genes with $GA, but as I said, I got a dimension error. Could you elaborate your point if possible coding demonstration is possible? > cut down exprs_mat with the shortlist of gen ...
written 3 hours ago by Jurat Shahidin60
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... @karl.stamm, @Asaf , @RamRS: As you suggested, I tried `limma::lmFit` where I set `ano$GA` as a covariate, here is my new attempt: library(limma) fit <- limma::lmFit(exprs_mat, design = model.matrix( ~ ano$GA) fit <- eBayes(fit) topTable(fit, coef=2) then I am expecting to ...
written 2 days ago by Jurat Shahidin60
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... interesting point. What I am going to do is to get a reduced dimension of expression set for the training ML model. if I use `limma` linear model, how can I produce a sub expression matrix (set of filtered genes)? Could you elaborate your point with possible coding demonstration instead? ...
written 3 days ago by Jurat Shahidin60
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... That's not what I am trying to do at that moment. Do you have better idea for what I asked in my post? Thanks ...
written 3 days ago by Jurat Shahidin60
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Comment: C: PCA plot from read count matrix from RNA-Seq
... @Kevin Blighe: Thanks for your contribution to Biostars community, this thread could be a good tutorial for PCA analysis series. ...
written 4 days ago by Jurat Shahidin60
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... Thanks for your reply. I intend to filter out genes in the gene expression matrix `expr_mat` by using correlation value (only keep highly correlated genes), and expected sub expression matrix should have same data structure as `expr_mat`. Do you have a possible idea to make this happen? Thank you I ...
written 4 days ago by Jurat Shahidin60
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Comment: C: How to filter out probsets and genes from Affymetrix microarray expression data
... Thanks for your community effort, I would this keep in mind in my future post. ...
written 4 days ago by Jurat Shahidin60
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Comment: C: How to filter out probsets and genes from Affymetrix microarray expression data
... I should avoid cross post, thanks for your reminding. Do I need to remove my post or just bring my attention next time? ...
written 4 days ago by Jurat Shahidin60
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How to correctly filer out gene expression matrix by measuring Pearson correlation coefficients?
... Hi I found @Kevin Blighe [answer][1] for finding Pearson correlation coefficients between a list of genes, and want to learn this solution on my problem. Basically, I have Affymetrix gene level expression matrix (genes in the rows and sample ID on the columns), and I have annotation data of microar ...
limma microarray gene-expression written 4 days ago by Jurat Shahidin60

Latest awards to Jurat Shahidin

Voter 4 days ago, voted more than 100 times.
Autobiographer 14 days ago, has more than 80 characters in the information field of the user's profile.
Popular Question 13 months ago, created a question with more than 1,000 views. For How to efficiently reuse and optimize same code block in wrapper function?
Popular Question 15 months ago, created a question with more than 1,000 views. For Any way coercing simple "list" to S4 "List" objects in R (with reproducible example)?
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