User: TriS

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TriS4.2k
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Posts by TriS

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Comment: C: Volcano plot for multiple clusters
... if those are the column names then you must have some sort of genes as row names. you gotta do a little bit of coding to define what genes belong to what cluster. 1- based on the cluster p.value and Log2FC define what belongs to what cluster 2- repeat that for all 20 clusters 3- color each gene base ...
written 6 months ago by TriS4.2k
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Answer: A: Volcano plot for multiple clusters
... or if you want to put them all together you can just color each group differently. library(ggplot2) ggplot(macrphage_list, aes(x = untreated.Log2.Fold.Change, y = -log10(untreated.P.Value), fill = myClusters)) + geom_point(size = 3) + geom_hline(yinterecept=-log10(10e-5)) + geom_vline(xi ...
written 7 months ago by TriS4.2k
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... this post is now pretty old, the data on cbioportal have been updated. that's why you see a difference ...
written 7 months ago by TriS4.2k
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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 14 months ago by TriS4.2k
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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 14 months ago by TriS4.2k
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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 14 months ago by TriS4.2k
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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 14 months ago by TriS4.2k
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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 14 months ago by TriS4.2k
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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 2.4 years ago by TriS4.2k
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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 2.4 years ago by TriS4.2k

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Popular Question 7 months ago, created a question with more than 1,000 views. For artifact/false peaks visible in wiggle files
Scholar 7 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 14 months ago, created an answer that has been accepted. For C: limma results topTable vs toptable differ
Scholar 14 months ago, created an answer that has been accepted. For A: How to split gene names in my list?
Great Question 19 months ago, created a question with more than 5,000 views. For retrieve full TCGA datasets from cBioportal with R
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Popular Question 20 months ago, created a question with more than 1,000 views. For artifact/false peaks visible in wiggle files
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Appreciated 22 months ago, created a post with more than 5 votes. For A: How to check whether two genomic regions contact in 3D?
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