User: Yunshun Chen

gravatar for Yunshun Chen
Yunshun Chen390
Reputation:
390
Status:
Trusted
Location:
Australia
Last seen:
1 day, 20 hours ago
Joined:
6 years, 11 months ago
Email:
y*****@wehi.edu.au

I maintain the edgeR and RnaSeqGeneEdgeRQL packages.

Posts by Yunshun Chen

<prev • 32 results • page 1 of 4 • next >
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Answer: A: problems when installing edgeR
... The current Bioconductor release version is 3.3, compatible with R 3.3. It seems you are not using an old version of R. Please update your R to the latest version before you try it again. ...
written 3.0 years ago by Yunshun Chen390
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Answer: A: Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE metho
... The Simes method was introduced and described in the following paper: R. J. Simes. An improved Bonferroni procedure for multiple tests of significance. Biometrika, 73(3):751~754, 1986. The Simes' method controls the family-wise error rate in the weak sense, i.e., only when all null hypotheses are ...
written 3.0 years ago by Yunshun Chen390
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Answer: A: Treat p > 1
... Thanks for reporting this. You're right. These p-values are not expected. The glmTreat is designed for two-sided hypothesis tests. The reason for such unexpected behaviors is that the observed fold change (FC) is closer to one FC boundary (threshold) but its likelihood is closer to the likelihood e ...
written 3.1 years ago by Yunshun Chen390
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Comment: C: Setting up the Design Matrix
... You're right. The two contrasts give you the results for the two comparisons of your interest. It is still possible to test for the main effect of temperature under the interaction model. However, the contrast is not as intuitive as what you would have using the one-way layout. The contrast would b ...
written 3.5 years ago by Yunshun Chen390
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Answer: A: Setting up the Design Matrix
... Your design looks correct and testing on coef=3 gives you the overall temperature effect. The first three questions can be answered by using this design. However, an interactive model (design) is required in order to test for the interaction effects between factors.   ...
written 3.5 years ago by Yunshun Chen390
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Comment: C: edgeR no residual degrees of freedom for a specific row of numbers in dispCoxRei
... Yes, it is a bug in the internal subsetting step. It's been fixed and it will be updated online soon. Note that the dispCoxReidInterpolateTagwise function uses min.row.sum=5 to filter out lowly expressed genes by default. Only genes (or rows) with total sum of counts above 5, which is the last row ...
written 3.5 years ago by Yunshun Chen390
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Comment: C: edgeR for with no Replicate
... It should be an index variable (a vector of row indices). ...
written 3.6 years ago by Yunshun Chen390
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Answer: A: edgeR for with no Replicate
... The error message reads: object 'housekeeping' not found. Clearly you haven't defined housekeeping. In the edgeR user's guide, it reads "For example, suppose that housekeeping is an index variable..." You can not simply copying the code from the user's guide and expect it to run without defining th ...
written 3.6 years ago by Yunshun Chen390
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Answer: A: ANOVA in EdgeR
... Your second method looks correct. The time effect and interaction effect contrasts in your first method don't make any sense. ...
written 3.7 years ago by Yunshun Chen390
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Comment: C: Different results in edgeR using simple vs GLM
... Good to know that there will be no egg on my face... ...
written 3.8 years ago by Yunshun Chen390

Latest awards to Yunshun Chen

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Questiond about the descrepancy between edgeR and limma-voom
Popular Question 2.8 years ago, created a question with more than 1,000 views. For edgeR: regarding Poisson distribution and goodness of
Voter 3.6 years ago, voted more than 100 times.
Scholar 3.8 years ago, created an answer that has been accepted. For A: negative values for trended dispersion with edgeR
Supporter 4.4 years ago, voted at least 25 times.
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For C: Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off

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