## User: menon_ankita

menon_ankita •

**30**- Reputation:
**30**- Status:
- New User
- Location:
- Last seen:
- 6 months ago
- Joined:
- 7 months, 1 week ago
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- m***********@hotmail.com

#### Posts by menon_ankita

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... Hello Dr. Blighe,
Thank you for the response. That is what I initially thought as well, but entering summary(res) gives me an output of something like this:
summary(res)
Length Class Mode
AADACL3 3 -none- numeric
AADACL4 3 -none- numeric
ACADM 3 ...

written 6 months ago by
menon_ankita •

**30**• updated 6 months ago by Kevin Blighe ♦**65k**0

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... Hello,
I am a student conducting a survival analysis in R. I am using 6,000 genes from 249 patients each, and am testing each gene separately by putting them in an individual Cox regression model. Here is the code that I have written in order to be able to test them all at the same time instead of ...

written 6 months ago by
menon_ankita •

**30**• updated 6 months ago by Kevin Blighe ♦**65k**0

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... I made histograms (thank you for the suggestion), and many of the genes seem to have a close to normal distribution (multiple are skewed though, none are perfect obviously). Will this skewedness in certain genes cause any issues in my analysis? Thanks for the help! ...

written 6 months ago by
menon_ankita •

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... Ok, thank you for all the help! ...

written 6 months ago by
menon_ankita •

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... Thanks for the response! Sorry for all the questions but - I did find cox results for every gene, and by plotting this do you mean plotting the distribution on something like this https://www.itl.nist.gov/div898/handbook/eda/section3/eda336.htm
(a Box-Cox plot)? ...

written 6 months ago by
menon_ankita •

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... Dr. Blighe - thank you for the response. I have clarified what I mean by "not working", sorry for the ambiguity. If I am dividing the RMA into expression ranges of tertiles, quartiles, etc., that is something I can do after the Cox regression and need only when I am plotting the survival graph, corr ...

written 6 months ago by
menon_ankita •

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... I am working on a survival analysis using the RMA normalized/transformed data of some cancer patients.
Here is a quick overview on RMA: http://www.molmine.com/magma/loading/rma.htm
As mentioned in the link above, RMA is already log-2 transformed and quantile normalized(skewed), so when I tried to ...

written 6 months ago by
menon_ankita •

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... I have done a Cox regression and found hazard ratios/p-values for the genes I want to graph, but I am not sure how I can put that on a curve without knowing what constitutes of high/low expression.
Here is what the values of my data look like in general:
AADACL3 5.26498
AADACL4 5.04068
ACADM 7.5495 ...

written 6 months ago by
menon_ankita •

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... Thanks for the very helpful reply!
Since you mentioned z-scores, I had a quick question. My data is RMA transformed/normalized (like this: http://www.molmine.com/magma/loading/rma.htm). When I attempted to calculate the global z-scores of my RMA normalized data, I was not getting a mean value of 0 ...

written 7 months ago by
menon_ankita •

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... Hello,
I am working on a project that seeks to identify potential biomarkers in neuroblastoma by using the tumor tissue expression data for 249 patients.
For my visualization/data analysis, I know that I can obviously use Kaplan-Meier curves to show the possibility/time of survival in relation to ...

written 7 months ago by
menon_ankita •

**30**• updated 7 months ago by dsull •**1.5k**#### Latest awards to menon_ankita

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