Moderator: karl.stamm

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karl.stamm3.5k
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Posts by karl.stamm

<prev • 465 results • page 1 of 47 • next >
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Comment: C: How do I install the R package on GitHub with bioconda
... What does bioconda have to do with R packages? What are you trying to do? You've asked how to install a lightbulb with a hammer, and I can't see any reasonable answer. ...
written 21 days ago by karl.stamm3.5k
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... I'm not going to provide the code. That's your job. It's basic data manipulation, that is a pre-requisite to work in this field. You can search other questions on this site or stackoverflow for specifics on how to subset a matrix in R. Our answers here are strategic, I have provided you many new ke ...
written 3 months ago by karl.stamm3.5k
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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. It's the matrix-sub-selection code that's broken. just cut down exprs_mat with the shortlist of genes, and you're done. ...
written 3 months ago by karl.stamm3.5k
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Comment: C: How to correctly filer out gene expression matrix by measuring Pearson correlati
... Take a look at the heatmap(cor(X)) and it should be square, symmetrical. Picking genes is tough because they are all strong on the diagonal. I bet every gene will be correlated to some part of the dataset. ...
written 3 months ago by karl.stamm3.5k
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Answer: A: How to correctly filer out gene expression matrix by measuring Pearson correlati
... In your comment: "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)?" I gather you're trying to find the genes that are highly correlated to each other. J ...
written 3 months ago by karl.stamm3.5k
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Comment: C: Why do so many biomarker based classifiers claim high accuracy but rarely used i
... Good points. Let's add points 5) apriori probability. If your system detects something with a 99% accuracy (1% FPR) and the general population carries the disease at <= 2%, then your new test is no better than blind chance! 6) no practical workflow. I've seen new techniques touted that detect ...
written 4 months ago by karl.stamm3.5k
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Answer: A: Best statistical test for genotype-specific gene expression analysis
... I would do a linear trend, summary(glm()) does ANOVA for the correlation. Envision a scatter plot, x is the number of G's, 0,1,2. y is your log(expression). Statistical power is your problem, if you're looking at lots of genes or lots of SNPs, you will have false-positive results somewhere. If yo ...
written 5 months ago by karl.stamm3.5k
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Comment: C: Shannon vs Simpson for TCR diversity estimation
... What are you trying to achieve when you say evaluate TCR status? If you're worried about technical errors, try technical replication. See what the error rates look like. ...
written 5 months ago by karl.stamm3.5k
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Comment: C: RNAseq: What's the accurate way to test whether a set of N genes is differential
... The sequencing depth may vary between groups, so plain read-counts are misleading. If your control had better RNA handling, because they were processed before lunch, it may have more reads overall, and then all genes appear downregulated. Tools made for differential expression know this and accoun ...
written 6 months ago by karl.stamm3.5k
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Comment: C: RNA-seq: Is it worth to analyze case vs control separately to have a % similarit
... And the experimental design. Do we care about differences in Ca1 and Ca2? By the design of the experiment those differences should be considered background noise. ...
written 6 months ago by karl.stamm3.5k

Latest awards to karl.stamm

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Popular Question 18 months ago, created a question with more than 1,000 views. For Can I run VEP on a VCF twice?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
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Appreciated 2.1 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Appreciated 2.4 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 2.6 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Appreciated 3.3 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq
Scholar 3.5 years ago, created an answer that has been accepted. For A: Is LOESS normalization done to each sample independently?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: multithreading in psiblast
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Correlated standard errors in DESeq2
Appreciated 3.5 years ago, created a post with more than 5 votes. For C: Why academic software is hard to install?
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Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Pathway Graphs for gene set from RNA-seq

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