User: Yunshun Chen

gravatar for Yunshun Chen
Yunshun Chen540
Reputation:
540
Status:
Trusted
Location:
Australia
Last seen:
3 days, 18 hours ago
Joined:
7 years, 4 months ago
Email:
y*****@wehi.edu.au

I maintain the edgeR and RnaSeqGeneEdgeRQL packages.

Posts by Yunshun Chen

<prev • 41 results • page 1 of 5 • next >
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Comment: C: adding "symbol" column in my differential expressed genes in EdgeR
... I can see how you defined `mp`. But have you ever checked what your `mp` actually is? You need to extract Endembl Ids from the `genes` column of `y$genes` and use it as `keys` in `mapIds()`. ...
written 27 days ago by Yunshun Chen540
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Answer: A: adding "symbol" column in my differential expressed genes in EdgeR
... You didn't show what your `mp` is. You set `keys=row.names(mp)` in `mapIds()`. But are they Ensembl Ids as required? Note that `mapIds()` is not an `edgeR` function. This questions is more related to how to use annotation packages such as `org.Hs.eg.db`. ...
written 27 days ago by Yunshun Chen540
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Answer: A: interpreting FC values from glmTreat, especially unshrunk log-fold-changes
... 1) The large unshrunk logFC values are not errors. They are computed in `glmFit()` with `prior.count=0`. The reason why they are so large is because the read counts of those transcripts are all zeros in one of the groups you are comparing. You don't need to deal with it yourself. The testing functio ...
written 4 weeks ago by Yunshun Chen540
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Answer: A: Nested Interaction in edgeR and composition bias
... I am not sure what your question is. If you are concerned about the composition biases between samples, then the edgeR scale normalization (eg. TMM) would take care of it. It has nothing to do with the interaction between your explanatory variables. If your question is about how to incorporate a c ...
written 6 weeks ago by Yunshun Chen540
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Answer: A: EdgeR DGElist - equal counts between treatment and control incorrectly give sign
... The reason for getting significant P-values is your upper-quartile normalization. Your count data is artificially constructed in the way that the upper-quartile of the `Trt` group is twice as much as that of the `Ctl` group. As a result, the normalization factors for the `Trt` samples are twice as m ...
written 7 weeks ago by Yunshun Chen540
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Answer: A: Can't get function plotExonJunc to work?
... The `plotExonJunc` function requires the coordinates of the exons/junctions to produce the plot. In particular, it requires the start and end positions, as well as the length and strand information, of each feature to be stored in `genes$Start`, `genes$End`, `genes$Length` and `genes$Strand` of the ...
written 9 weeks ago by Yunshun Chen540
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Answer: A: EdgeR - Complex design - contrasts/coefficients
... To construct a proper contrast, you need to understand the meaning of each coefficient first. In this particular design matrix, the `(Intercept)` represents the Healthy Patient 1 with no treatment. The coefficient `DiseaseDisease1` represents the **difference** between Disease1 and Healthy for Pati ...
written 12 weeks ago by Yunshun Chen540
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Answer: A: is our edgeR code doing what we think it does?
... You should always refer to the edgeR user's guide. There are several detailed case studies in the user's guide with complete R code and explanation which you can easily follow. We usually recommend the quasi-likelihood approach for differential expression analysis as we found it gives better FDR co ...
written 3 months ago by Yunshun Chen540
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Answer: A: edgeR DGEList and design matrix
... Is your `x` a count matrix? If so, have you performed filtering? Lowly expressed genes (especially with zero counts across all samples) can cause problems in dispersion estimation. You can perform filtering using the `filterByExpr()` function. ...
written 4 months ago by Yunshun Chen540
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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 3.4 years ago by Yunshun Chen540

Latest awards to Yunshun Chen

Popular Question 3.2 years ago, created a question with more than 1,000 views. For Questiond about the descrepancy between edgeR and limma-voom
Popular Question 3.2 years ago, created a question with more than 1,000 views. For edgeR: regarding Poisson distribution and goodness of
Voter 4.0 years ago, voted more than 100 times.
Scholar 4.2 years ago, created an answer that has been accepted. For A: negative values for trended dispersion with edgeR
Supporter 4.8 years ago, voted at least 25 times.
Teacher 5.1 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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