User: TriS

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TriS3.8k
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Posts by TriS

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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... see comments above where I addressed this question ...
written 8 weeks ago by TriS3.8k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... it's good practice to remove genes that have expression = 0 or very low expression in most samples. the % is up to you, this is an example, and I used 50% ...
written 8 weeks ago by TriS3.8k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... that's because you are trying to assign a variable starting with the square bracket, which in R is used to subset variables. I'd suggest to get familiar with R first, instead of copy-paste the code above. that will help you preventing lethal mistakes ...
written 8 weeks ago by TriS3.8k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... that will require quite a lil bit of coding, I'd suggest you to refine your question first and then contact a bioinformatician/statistician to help you coding it ...
written 8 weeks ago by TriS3.8k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... you have to select patients based on the expression of two genes. - choose your two genes - classify patients based on the expression of both (i.e. `tp53 > 2 & pi3k > 2`) - that will be your altered class - the rest is not altered. or you can also count patients that are altered for one an ...
written 9 weeks ago by TriS3.8k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this code is a guideline, not a copy and paste document. I'd suggest you to read a bit more about basic R usage and survival analysis before digging into this. it'll be time well spent ...
written 17 months ago by TriS3.8k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... you have to group patients using the parameters you chose (i.e. groups) instead of gene expression altered/not altered. I'd suggest you to read a bit more about basic survival analysis and how it works before digging into this one ...
written 17 months ago by TriS3.8k
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Comment: C: How to visualize Proteome Networks
... this might help: https://www.hindawi.com/journals/abi/2017/1278932/ ...
written 18 months ago by TriS3.8k
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Comment: C: PCA Tools to analyse RNA-seq data
... the linked version is a web-based application. the desktop application is a standalone java-based version ...
written 19 months ago by TriS3.8k
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Comment: C: The way to get the all p-value of functionally annotated categories from DAVID?
... as comment to DAVID, it has been updated to the [6.8 version][1] on Oct 2016 [1]: https://david.ncifcrf.gov/ ...
written 19 months ago by TriS3.8k

Latest awards to TriS

Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?
Great Question 6 months ago, created a question with more than 5,000 views. For retrieve full TCGA datasets from cBioportal with R
Popular Question 7 months ago, created a question with more than 1,000 views. For artifact/false peaks visible in wiggle files
Appreciated 10 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Popular Question 10 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 10 months ago, created a question with more than 1,000 views. For indel position in repetitive regions
Appreciated 11 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
Popular Question 11 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
Popular Question 12 months ago, created a question with more than 1,000 views. For breakdancer - cfg creation and chi square problem
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Popular Question 17 months ago, created a question with more than 1,000 views. For filtering pileup file with samtools for SomaticSniper
Scholar 20 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Scholar 22 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Diagnose my daughter?
Scholar 23 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How to split gene names in my list?
Popular Question 24 months ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Popular Question 2.1 years ago, created a question with more than 1,000 views. For pros- and cons- : programming skills vs. GUI
Scholar 2.1 years ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
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Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: How to check whether two genomic regions contact in 3D?

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