User: TriS

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TriS2.4k
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Posts by TriS

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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this question goes beyond what's described in this tutorial, you should start a new question in Biostar for that. ...
written 14 days ago by TriS2.4k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... it seems that there is a problem on the comment above where some brackets don't show up. pv <- ifelse ( is.na(s1),next,(round(1 - pchisq(s1$chisq, length(s1$n) - 1),3)))[[1]] ...
written 21 days ago by TriS2.4k
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Answer: A: Is it OK to select a small subset of expression data for statistical testing?
... it all depends from your rationale for choosing those genes. for example, if you choose genes that are g-protein coupled receptors and do functional enrichment analyses, you will find genes that are part of the g-protein coupled receptor pathways...and therefore your analysis will be futile. othe ...
written 5 weeks ago by TriS2.4k
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Comment: C: Heatmap: how to just show significantly differentially expressed transcripts in
... hi Farbod, I am not sure how to do that, it might be useful to start a new thread with that question since it's drifting away from your initial problem ...
written 5 weeks ago by TriS2.4k
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Comment: C: Heatmap: how to just show significantly differentially expressed transcripts in
... 1. I personally don't know a way to add a second column with the different rownames as text. 2. never used it 3. the "%in%" command allows you to look for something into something else, and returns the index with the position(s) of the element(s) in the array you searched. in that case I assumed ...
written 5 weeks ago by TriS2.4k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... 1. you can use either, I just picked one. this tutorial is a guideline, not a rule 2. I didn't know that was available at the time of this tutorial, thank you for bringing that up, it is very useful 3. this post is almost a year and a half old, I would expect some differences in the events 4. be ...
written 5 weeks ago by TriS2.4k
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Comment: C: Heatmap: how to just show significantly differentially expressed transcripts in
... you don't see the sample names because you don't have rownames :) ...
written 5 weeks ago by TriS2.4k
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Comment: C: Heatmap: how to just show significantly differentially expressed transcripts in
... what does `head(my_matrix)` return? ...
written 5 weeks ago by TriS2.4k
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Comment: C: Heatmap: how to just show significantly differentially expressed transcripts in
... 1- you can use `pheatmap(myData,scale="row")` 2- use `color=colorRampPalette(c("#fee8c8", "#fdbb84", "#e34a33"))(100),breaks=seq(-2,2,length=100)` within the pheatmap function 3- without your code it's impossible to say why you get the error ...
written 5 weeks ago by TriS2.4k
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Answer: A: Heatmap: how to just show significantly differentially expressed transcripts in
... > 1) How can I do it? is it just by selecting those 88 transcripts TMM > value and used them as input in R heatmap script? create a matrix containing only the genes you are interested in and use that for your heatmap. you can easily do that in R (assuming genes in rows and samples in columns) ...
written 5 weeks ago by TriS2.4k

Latest awards to TriS

Appreciated 14 days ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Appreciated 26 days ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Scholar 5 weeks ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Epic Question 4 months ago, created a question with more than 10,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 4 months ago, created a question with more than 1,000 views. For sample size, normality assumption, t.test/anova for DEG analysis
Gold Standard 5 months ago, created a post with more than 25 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 7 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Popular Question 7 months ago, created a question with more than 1,000 views. For TCGA survival analysis with z-scores all samples altered
Good Answer 8 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 8 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Great Question 9 months ago, created a question with more than 5,000 views. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Popular Question 10 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 10 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Librarian 12 months ago, created a post with more than 10 bookmarks. For Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Popular Question 12 months ago, created a question with more than 1,000 views. For Plot average methylation levels across TSS region
Scholar 13 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 13 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Guru 14 months ago, received more than 100 upvotes.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?

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