User: Jurat Shahidin

gravatar for Jurat Shahidin
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Location:
Chicago, IL, USA
Website:
https://cs.uic.edu/
Last seen:
1 month ago
Joined:
3 years, 9 months ago
Email:
j******@uic.edu

I am a Ph.D. student in Artificial Intelligence, Machine learning, Bioinformatics. 

Posts by Jurat Shahidin

<prev • 125 results • page 1 of 13 • next >
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Any recommended workflow for incrementally selecting top ranked genes by using mRMR feature selection?
... Hi: I am using Affymetrix microarray gene expression data, and I am trying to do feature selection by using different methods. However, I am quite interested in one of the popular methods for feature extraction - minimum redundancy maximum relevance. I found `CRAN` package, `Parallelized Minimum Re ...
microarray gene-filtering mrmr parallel-processing bioconductor-package written 3 months ago by Jurat Shahidin • 70
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Comment: C: How can I overcome the error of "No residual degrees of freedom in linear model
... bingo, I just fixed this by taking your opinion, but why I should include `Batch` instead of `SampleID`? I am a newbie for differential expression analysis, so this is not crystal clear to me yet. Could you give extended comments on your proposal? I want to learn? what else I have to try for `design ...
written 3 months ago by Jurat Shahidin • 70
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How can I overcome the error of "No residual degrees of freedom in linear model fits"?
... Hi: I am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. However, I have `pheno` metadata for the experiment observations. **data that I used**: > ...
microarray limma error written 3 months ago by Jurat Shahidin • 70 • updated 3 months ago by Dario Strbenac • 1.5k
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Comment: C: Any efficient workaround to identify highly variable genes in Affymetrix microar
... yes, I do highly endorse your solution and already accepted as an answer. Here I just show what I did after learning your solution because I am still learning gene-expression analysis, so it could be good practice for me to come up my own solution. please don't me wrong, I could delete my solution i ...
written 4 months ago by Jurat Shahidin • 70
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Comment: C: Any efficient workaround to identify highly variable genes in Affymetrix microar
... I do follow community rule and thanks again for your clarification, appreciated. ...
written 4 months ago by Jurat Shahidin • 70
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Answer: A: Any efficient workaround to identify highly variable genes in Affymetrix microar
... Thanks for Gordon's help, I come across with my simple solution as follow: SD <- apply(eset_HTA20,1, sd) CV <- base::sqrt(exp(SD^2)-1) eset_filtered <- eset_HTA20[CV > quantile(CV, probs = 0.1),] ...
written 4 months ago by Jurat Shahidin • 70
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Comment: C: Any efficient workaround to identify highly variable genes in Affymetrix microar
... Thanks, I figured out this and I'll keep this in my mind later. FYI, I just add my own answer, thanks for your community contribution. ...
written 4 months ago by Jurat Shahidin • 70
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Comment: C: Any efficient workaround to identify highly variable genes in Affymetrix microar
... Could you elaborate your point please? My intention is to use the coefficient of variation for each gene (a.k.a, probe), to toss away low expressed genes, ultimately to obtain expression matrix with only highly expressed genes in the experiment. My downstream analysis, after properly deal with Af ...
written 4 months ago by Jurat Shahidin • 70
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Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
... Hi: I am experimenting preprocessed Affymetrix microarrays expression data matrix (Affymetrix probe-sets in rows (32830 probesets), and RNA samples in columns (735 samples)) for my downstream analysis. Here is how the data looks like: > dim(eset_HTA20) [1] 32830 735 ## load assayD ...
microarray genefilter limma deseq2 written 4 months ago by Jurat Shahidin • 70
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Comment: C: How to find out the genes that changes in expression by using gene level express
... @Guido Hooiveld : Thanks for your response. If the loaded expression matrix as Affymetrix probe-sets in rows, RNA samples in columns, how can I factor out the matrix in gene expression level matrix instead? Because standard Affymetrix microarrays workflow starts with row cell files, while in my cas ...
written 4 months ago by Jurat Shahidin • 70

Latest awards to Jurat Shahidin

Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.
Great Question 17 months ago, created a question with more than 5,000 views. For Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
Great Question 17 months ago, created a question with more than 5,000 views. For Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
Epic Question 17 months ago, created a question with more than 10,000 views. For Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Popular Question 17 months ago, created a question with more than 1,000 views. For How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
Popular Question 17 months ago, created a question with more than 1,000 views. For do.call error "second argument must be a list" with GRanges object [closed]
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to conditionally combine IntegerList in the DataFrame more elegantly?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
Centurion 3.5 years ago, created 100 posts.
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Scholar 3.5 years ago, created an answer that has been accepted. For A: How can I get global Fisher score for overlap of 3 GRanges object by element-wis
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to sort set of GRanges object in the list by increasing order?
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to avoid repeated overlap pair for GRanges object in grid?
Student 3.5 years ago, asked a question with at least 3 up-votes. For Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
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