User: Steven Lakin

gravatar for Steven Lakin
Steven Lakin1.3k
Reputation:
1,270
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Trusted
Location:
Fort Collins, CO, USA
Last seen:
1 day, 11 hours ago
Joined:
1 year, 8 months ago
Email:
S***********@colostate.edu

Veterinary/PhD student at Colorado State University.  My research applies statistics and machine learning to problems in biomedical science and public health.  My computational experience is in data mining/data science, statistics, machine learning, bioinformatics algorithms, programming, genomics, and transcriptomics.  Wetlab experience includes NGS library prep, PCR, and culture-based methods.  Interests include pathogenesis of infectious disease, antimicrobial resistance, public health, and epidemiology.

 

https://github.com/lakinsm

Posts by Steven Lakin

<prev • 116 results • page 1 of 12 • next >
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Comment: C: Multivariable linear regression using Limma package; Model Matrix design
... Just to re-iterate: this is incorrect; contac onet of us if you're intersted in using our tools. ...
written 1 day ago by Steven Lakin1.3k
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Comment: C: Multivariable linear regression using Limma package; Model Matrix design
... To elaborate on this; don't do this. Do instead '0 + mainEffect1 + covariate1) ...
written 1 day ago by Steven Lakin1.3k
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Comment: C: Multivariable linear regression using Limma package; Model Matrix design
... Standard regression analysis for count data is based on modeling expression values as a function of explanatory variables that are part of the experimental design: y ~ 0 + effect1 + effect2 + (1 | effect 3) For example. Typically, we want to explain the expression values as a function of some sys ...
written 1 day ago by Steven Lakin1.3k
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Comment: C: Multivariable linear regression using Limma package; Model Matrix design
... Right, which is what we product based on standard logic. Let me know if you're interested in the standard experimental designs. ...
written 1 day ago by Steven Lakin1.3k
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Comment: C: Help with linear regression model design
... What you did in your very first design (not this answer), where you found no DE genes, was correct. What you've done above is incorrect; stick with your intuition on this one. It's not uncommon for groups to be insignificant on DE analysis, especially with cancer expression analysis. ...
written 3 days ago by Steven Lakin1.3k
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Answer: A: Help with linear regression model design
... It's nice that you were able to see that the pairwise analyses in DESeq and limma are equivalent to regression and then fitting on the contrasts by hand; they are exactly the same process, only DESeq and limma handle them for you in the background if you specify the model in the way you originally d ...
written 3 days ago by Steven Lakin1.3k
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Comment: C: Multivariable linear regression using Limma package; Model Matrix design
... I think I understand what you're trying to do now. Apologies; it is the first time I've seen someone request this in bioinformatics, as it is somewhat strange to model this way. What you will have to do is construct your model matrix like so (this assumes your probe matrix is, by native format, in ...
written 3 days ago by Steven Lakin1.3k
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Answer: A: Multivariable linear regression using Limma package; Model Matrix design
... Programs like Limma force the gene expression values to be the response variable because that is the correct way to model it: lmFit(probe_matrix, design = model.matrix( ~ 0 + Disease phenotype + covariate ) This will calculate regression coefficients for disease phenotype and the covariate as ...
written 3 days ago by Steven Lakin1.3k
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Comment: C: Unranked nodes in NCBI's taxonomic tree
... Hi Brian. Do you happen to have a repository for the node pruning tool? It sounds useful. ...
written 4 days ago by Steven Lakin1.3k
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Answer: A: Unranked nodes in NCBI's taxonomic tree
... In short, I think your method is fine. Do proceed with caution in terms of making comparisons though; the main problem with unranked nodes is that they aren't comparable across the taxonomic tree. This is an issue for all who are developing or testing microbiome classifiers, and there likely isn't ...
written 5 days ago by Steven Lakin1.3k

Latest awards to Steven Lakin

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Scholar 5 days ago, created an answer that has been accepted. For A: Allele count from factor variable in R
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Appreciated 6 days ago, created a post with more than 5 votes. For C: Fisher's exact test gives p-value 0
Scholar 8 days ago, created an answer that has been accepted. For A: Allele count from factor variable in R
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Centurion 13 days ago, created 100 posts.
Scholar 27 days ago, created an answer that has been accepted. For A: Allele count from factor variable in R
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Good Answer 29 days ago, created an answer that was upvoted at least 5 times. For A: Is it OK to select a small subset of expression data for statistical testing?
Appreciated 29 days ago, created a post with more than 5 votes. For C: Fisher's exact test gives p-value 0
Guru 29 days ago, received more than 100 upvotes.
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Retrieving specific columns from clinicaltrial.gov using R
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Fisher's exact test gives p-value 0
Appreciated 4 months ago, created a post with more than 5 votes. For C: Fisher's exact test gives p-value 0
Scholar 6 months ago, created an answer that has been accepted. For A: Allele count from factor variable in R
Appreciated 7 months ago, created a post with more than 5 votes. For C: Fisher's exact test gives p-value 0
Supporter 7 months ago, voted at least 25 times.
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Fisher's exact test gives p-value 0
Scholar 8 months ago, created an answer that has been accepted. For A: Allele count from factor variable in R
Scholar 8 months ago, created an answer that has been accepted. For A: Allele count from factor variable in R
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Make 2 boxplot from a data frame by plotting values in 1 row with different col
Scholar 9 months ago, created an answer that has been accepted. For A: Allele count from factor variable in R

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