User: tujuchuanli
tujuchuanli • 30
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Posts by tujuchuanli
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... Hi,
I have a set of genes (10 genes which are belonged to the same pathway). I want to explore the expression profile of these genes in BRCA datasets.
In additionally, I want to explore whether these genes or some of these genes could divide cancer samples into subgroups. In each subgroup the comb ...
written 7 weeks ago by
tujuchuanli • 30
• updated
7 weeks ago by
finswimmer ♦ 11k
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... Hi,
I did differentially expression (DE) analysis on TCGA datasets and identified several DE genes. During my paper review, one of reviewers insisted on the validation of DE genes by experiment.
To be honest, I do not have place, equipment and so on to do this validation. So I have a Plan-B which ...
written 10 weeks ago by
tujuchuanli • 30
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C: question about gene signatures
... > Yes, logged data is better. However, the data in your histogram does
> not appear to be logged (?).
I think there is a missleading. The histogram is response value, which is mutation load not expression of gene (the expression value is used as predictor).
Do you mean I should try log-transf ...
written 10 weeks ago by
tujuchuanli • 30
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C: question about gene signatures
... Do you mean that I should use TMM normalized RNA-seq counts without log-transformed as predictor value? In survival analysis it is recommanded to use log transformed TMM normalized RNA-seq counts. what is the difference? ...
written 10 weeks ago by
tujuchuanli • 30
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Comment:
C: question about gene signatures
... The response value is mutation load. It is calculated as the total number of miss-sense mutations in CDS region per patient. Here I want to explore the expression profile correlated to it. What I can say is that the distribution of this value is similar with previous works. It is hard to say how to ...
written 10 weeks ago by
tujuchuanli • 30
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C: question about gene signatures
... Below is the histogram of my count data (response value):
It is generated by "hist" function
![enter image description here][1]
[1]: http://img.027cgb.com/613969/QQ%E6%88%AA%E5%9B%BE20190107225752.png ...
written 10 weeks ago by
tujuchuanli • 30
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Comment:
C: question about gene signatures
... Hi Kevin,
Thank you for your replying, two additional questions:
1. I used the best predictors from “cv.glmnet” function to build the new model using “glm” function, then I summarized the regression using “summary” function. I found that not all predictors here are significant. Can I perform secon ...
written 10 weeks ago by
tujuchuanli • 30
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Comment:
C: question about gene signatures
... Hi Kevin,
It is very nice of you to supply such precious materials to me. I have some questions after reading your post.
1. My response value is continuous value just like Chip-seq reads counts and my predictive values are expression of genes. Should I use “poisson” instead of “multinomial” in “cv ...
written 10 weeks ago by
tujuchuanli • 30
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... Hi,
Here I have a feature which was measured in patients from the BRCA dataset of TCGA (each patient has one value for this feature). It is a continuous variable. I want to find a set of genes measured by gene expression of RNA-seq which is highly correlated with this feature (so-called “gene signa ...
written 11 weeks ago by
tujuchuanli • 30
• updated
10 weeks ago by
Kevin Blighe ♦ 39k
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Comment:
A: question about survival analysis
... Thank you for your replying, Kevin~~
Following your suggestion that interaction is a bit misleading, I`ve changed my words.
I considered that these gene pairs as the pairs which combination of two genes with different expression level correlated with different survival outcome, is it better?
BTW, ...
written 12 weeks ago by
tujuchuanli • 30
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