User: Raheleh
Raheleh • 120
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Posts by Raheleh
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... Thank you cpad. I want to have risk table as well. I already tried to do it by annotate function. However, when I use annotate, risk table goes.
Do you know how to keep risk table and HR together?
Thank you!
...
written 5 days ago by
Raheleh • 120
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... Hi, I plot the KM for my data. This is the script:
ggsurvplot(survfit(recsurv~T1_signature, data = MSKCC), size = 1,
palette = c("#E7B800", "#2E9FDF"),
conf.int = FALSE,
pval = TRUE,
risk.table = TRUE,
risk.table ...
written 6 days ago by
Raheleh • 120
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Comment:
C: Problem with UpSetR result
... Thanks, but I got this error:
> Error in `[.default`(data, sets) : invalid subscript type 'list' ...
written 6 days ago by
Raheleh • 120
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... Hello, I have a dataframe with 3 variable and 56 observations which are just 1 and 0. Instead of venn diagram I am useing UpsetR package to find the intersections between variables. This is the [link][1].
This is my script:
dat <- read.delim("dat.csv", sep = ",", stringsAsFactors = FALSE)
...
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Comment:
C: How to plot GSEA result?
... Many thanks @gabrit. I did it.
I am trying to add title for my plot.
Do you know how I can do it? ...
written 21 days ago by
Raheleh • 120
6
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... Hello there,
I did standard GSEA for my microarray expression data. As I found out GSEA tools provide GSEA plot just for top 20 of enriched pathways. How can I provide plot for other pathways which are also significantly enriched (adj-pval < 0.05) in my dataset based on GSEA?
I am trying *fgsea ...
written 22 days ago by
Raheleh • 120
• updated
21 days ago by
Barry Digby • 230
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... Thank you Kevin for your prompt reply. But the problem is still there. ...
written 8 weeks ago by
Raheleh • 120
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... Many thanks Kevin for this great tutorial. I went through all the step (just for up-regulated genes) and the image that I got at the end is like this. Why at the bottom of the right side there are some muddled text. How can I remove them? I tried but I couldn't. I really appreciate your time and he ...
written 8 weeks ago by
Raheleh • 120
0
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... Thank you for your reply. But, I got confused. You say " ***a greater positive value means a stronger positive influence**.*"
If I'm not mistaken you mean a gene with a greater positive value of coefficient (for example in my case, FLNA and SLC2A3 and MAP7D2 respectively in relapse data) is a bette ...
written 11 weeks ago by
Raheleh • 120
0
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... Many thanks Jean-Karim for your explanation. I still couldn't understand the meaning of those **dots** . could you please explain more? I am looking for the best predictor genes which can predict patients at risk of relapse. Based on the result that I got above, which genes are the best predictors?
...
written 12 weeks ago by
Raheleh • 120
Latest awards to Raheleh
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For The result of differential gene expression analysis should be extracted based on adj.p.value ?
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Popular Question
9 months ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
Student
13 months ago,
asked a question with at least 3 up-votes.
For Why some probes have "NA" for gene symbol and Entrez ID?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Why some probes have "NA" for gene symbol and Entrez ID?
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