User: menon_ankita

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menon_ankita30
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Posts by menon_ankita

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Obtaining P Values from Cox Regression in R
... 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_ankita30 • updated 6 months ago by Kevin Blighe65k
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Obtaining P Values from Cox Regression in R
... 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 ...
p-value survival-analysis cox-regression rna-seq written 6 months ago by menon_ankita30 • updated 6 months ago by Kevin Blighe65k
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Comment: C: Please Recommend Potential Graphs to Use For Gene Expression Survival Analysis
... 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_ankita30
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Comment: C: RMA Transformed Data: How to Determine Low/High Expression
... Ok, thank you for all the help! ...
written 6 months ago by menon_ankita30
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Comment: C: Please Recommend Potential Graphs to Use For Gene Expression Survival Analysis
... 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_ankita30
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Comment: C: RMA Transformed Data: How to Determine Low/High Expression
... 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_ankita30
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RMA Transformed Data: How to Determine Low/High Expression
... 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 ...
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Comment: C: Please Recommend Potential Graphs to Use For Gene Expression Survival Analysis
... 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_ankita30
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Comment: C: Please Recommend Potential Graphs to Use For Gene Expression Survival Analysis
... 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_ankita30
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Please Recommend Potential Graphs to Use For Gene Expression Survival Analysis
... 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 ...
R kaplan-meier gene-expression survival-analysis written 7 months ago by menon_ankita30 • updated 7 months ago by dsull1.5k

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