User: Jurat Shahidin
Jurat Shahidin • 60
- 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
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... 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 Shahidin • 60
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... > Your topTable() should have the genes that correlate nicely to $GA
I am trying to get these nicely correlated genes with $GA, but as I said, I got a dimension error. Could you elaborate your point if possible coding demonstration is possible?
> cut down exprs_mat with the shortlist of gen ...
written 3 hours ago by
Jurat Shahidin • 60
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... @karl.stamm, @Asaf , @RamRS:
As you suggested, I tried `limma::lmFit` where I set `ano$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 Shahidin • 60
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... 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 Shahidin • 60
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... 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 Shahidin • 60
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... @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 Shahidin • 60
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... 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 Shahidin • 60
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... Thanks for your community effort, I would this keep in mind in my future post. ...
written 4 days ago by
Jurat Shahidin • 60
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... 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 Shahidin • 60
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... 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 ...
written 4 days ago by
Jurat Shahidin • 60
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For Any alternative (free, open source tool) for Geneious software for phylogenetic analysis?
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