User: TriS

gravatar for TriS
TriS2.7k
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United States, Buffalo
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Posts by TriS

<prev • 303 results • page 1 of 31 • next >
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Comment: C: Problem with Manhattan plot
... how do your data look? what's the code that you used? I suppose you are using R for the plot? what does the image look like (we can't see it, or at least I can't)? hard to help without info ...
written 12 days ago by TriS2.7k
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Answer: A: DESeq2: Find differentially expressed genes specific to one condition
... I had a similar situation, I used limma, not DESeq2 but the concept is the same. the first thing I did was to use your approach #1, which worked fine. then I started working on the contrast matrix. let's say your data look like > data A A B ...
written 12 days ago by TriS2.7k
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Answer: A: RNA-seq analysis with quantitative traits
... this is also a good read for your analysis [RNA-seq analysis for detecting quantitative trait-associated genes][1] [1]: https://www.nature.com/articles/srep24375 ...
written 13 days ago by TriS2.7k
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Comment: C: BWA: Why paired reads mapped to different chromosome?
... fusion gene event could cause that. are those cancer samples? ...
written 13 days ago by TriS2.7k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... hmmm, ok, try to run `s1` and `summary(s1)` you should get something like the following > s1 Call: survdiff(formula = f ~ a) N Observed Expected (O-E)^2/E (O-E)^2/V a=1 77 44 45.5 0.0464 0.0794 a=2 106 69 67.5 0.0312 0.0794 ...
written 24 days ago by TriS2.7k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... how does your `s1` object look? ...
written 25 days ago by TriS2.7k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... i'll modify it now...I'm not sure why that happens. it seems that some parenthesis are cut off. my apologies for the inconvenient ...
written 25 days ago by TriS2.7k
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Comment: C: how I can come up with a permanent error
... can you share the miRNA.txt file? also any(duplicated(colnames(mycounts))) [1] FALSE shouldn't it be any(duplicated(rownames(mycounts))) and therefore which(duplicated(mycounts[,1])) ...
written 4 weeks ago by TriS2.7k
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Comment: C: retrieve full TCGA datasets from cBioportal with R
... they are not the same "processed". cBiportal gives you expression data in tumor compared to normal. TCGA firehose gives you level 3 TCGA RNASeq data (aligned, mapped, normalized RPKM/FPKM gene/exon/etc level), which cBioportal does not. ...
written 4 weeks ago by TriS2.7k
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Answer: A: select DE genes
... once you have a clear idea of how you want to compare your groups and you did a good Google search on how to do it, this is one of my favorite tutorials from Bioconductor: https://www.bioconductor.org/help/workflows/RNAseq123/ however, it requires some knowledge of R. also, don't forget to look a ...
written 5 weeks ago by TriS2.7k

Latest awards to TriS

Scholar 10 days ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Popular Question 12 days ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Scholar 5 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 8 months ago, created a question with more than 10,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 8 months ago, created a question with more than 1,000 views. For sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 9 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 11 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 12 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Great Question 13 months ago, created a question with more than 5,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 14 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 14 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Appreciated 16 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Librarian 16 months ago, created a post with more than 10 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?

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