User: dodausp

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dodausp110
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Denmark/Copenhagen/BRIC
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Posts by dodausp

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Finding the best combination of covarites in a multivariate linear regression
... Hi, Martombo Thanks for the feedback. And you are right, maybe my question did not conceive the whole concept I was thinking about. I am putting down an example so I hope I can get my message across better this time. So, say I have a data frame with 196 rows (sample ID) by 32 columns (gene names). ...
written 5 weeks ago by dodausp110
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Comment: C: Exploring association between genes by their expression
... Thank you, genomax. The reason why I posted here it was because this is a follow-up question from the original question in this post. But you are right. Thank you for the info. ...
written 7 weeks ago by dodausp110
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Finding the best combination of covarites in a multivariate linear regression
... Hi! This post is sort of a follow-up questions from this previous thread: [Exploring association between genes by their expression][1]. Briefly, say I have a list of candidate genes whose expressions showed (1) to be associated with overall survival (OS) (Cox regression), and (2) also associated a ...
overall survival gene expression linear model R written 7 weeks ago by dodausp110
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Comment: A: Exploring association between genes by their expression
... Hi again! This time, going a bit further with the analysis. I have performed the Cox regression with lasso penalty (`glmnet()`) and cross-validated with `cv.glmnet()`, and came out with a total of 31 candidates. To my understanding, and by plotting the K-M curves, those candidates show the best ass ...
written 7 weeks ago by dodausp110
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Comment: C: Exploring association between genes by their expression
... Yes! We did quite on a very similar way. Thanks a lot! (: I now have another question, that I am posting below as an "answer". That because it is downstream to what I want to do next. ...
written 7 weeks ago by dodausp110
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Comment: C: Exploring association between genes by their expression
... Maybe I figured that out. These were the steps: #First, converting any "0" in my OS (time in months) column to a very small number #For some reason the glmnet() function doesn't like it shortlist_cox$OS <- ifelse(shortlist_cox$OS==0, 0.001, shortlist_cox$OS) #Then creating e ...
written 8 weeks ago by dodausp110
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Comment: C: Exploring association between genes by their expression
... Hi, Kevin Again, your insights are spot on. Thanks a lot! In regards to cutting down the amount of variables, I would like to run the following analysis with those candidates because they are already on a threshold of p<0.005. At least, I would like to give it a go on this first. I have read a bi ...
written 8 weeks ago by dodausp110
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Comment: A: Should We Have A Native Biostar Mobile App?
... I think that is a GREAT idea! ...
written 9 weeks ago by dodausp110
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Exploring association between genes by their expression
... Hi, everyone I have a dataset on gene expression of cancer patients, which I performed Cox regression for each gene to find their association with overall survival. I came down to a shortlist of around 1,500 candidates. To my mind, if one could show which genes from that shortlist are associated wi ...
R gene expression correlation linear model written 9 weeks ago by dodausp110
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Comment: C: Performing univariate and multivariate logistic regression in gene expression da
... I believe that was exactly my problem. I started with around 1,200 variables (genes), going down to 47 - cutting off by p-value. It worked on the last case. In that case, would you recommend to keep my list of selected variables as low as possible, or would it be worth trying the other methods - bay ...
written 3 months ago by dodausp110

Latest awards to dodausp

Supporter 9 weeks ago, voted at least 25 times.
Popular Question 6 months ago, created a question with more than 1,000 views. For How to set the control group in microarray analysis from illumina data?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Drug interaction not running in MAFtools
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieving miRNA data from Firehose by using RTCGAToolbox
Popular Question 9 months ago, created a question with more than 1,000 views. For Biobase not running in R 3.5.0

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