User: tujuchuanli
tujuchuanli • 40
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Posts by tujuchuanli
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... Hi,
I want to identify differential genes (DEG) in TCGA dataset (cancer samples vs normal samples) by combination of `edgeR` and `sva` (get rid of batch effect by `sva`). The following is my code and I am not sure if it is ok or not. Could you please help me to check the code and give me some sugge ...
written 3 months ago by
tujuchuanli • 40
• updated
3 months ago by
ATpoint ♦ 19k
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... Hi,
I did differentially expression (DE) analysis on TCGA datasets and identified DE genes by edgeR (DE genes between cancer and normal samples). During my paper review, one of reviewers raised the question which is how to deal with batch effect.
I checked the edgeR manual. It could deal with batc ...
written 3 months ago by
tujuchuanli • 40
• updated
3 months ago by
kristoffer.vittingseerup • 2.0k
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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 5 months ago by
tujuchuanli • 40
• updated
5 months 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 6 months ago by
tujuchuanli • 40
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340
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Comment:
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 6 months ago by
tujuchuanli • 40
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340
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Comment:
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 6 months ago by
tujuchuanli • 40
0
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340
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1
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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 6 months ago by
tujuchuanli • 40
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340
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Comment:
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 6 months ago by
tujuchuanli • 40
0
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340
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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 6 months ago by
tujuchuanli • 40
0
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1
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340
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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 6 months ago by
tujuchuanli • 40
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For Correlation between gene expression and methylation
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