User: Yanzhu Lin

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Yanzhu Lin110
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Posts by Yanzhu Lin

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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Thompson, Is $sample the way to get the sample weight? Thanks, Yanzhu ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Thompson, I would like to do some analysis using the sample weights generated by  voomWithQualityWeights(), is there a way that I could export the sample weights from  voomWithQualityWeights()? I took a look at supplemental material (http://bioinf.wehi.edu.au/voomWithQualityWeights/mixture/mixt ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Gordon, One more question about the design matrix used for option "var.design" in the voomWithQualityWeights(). I am not sure whether I used this function in the correct way and would like to double check with you. For example, if I have three factors: A (four levels), B (three levels), C ( two ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Thompson, I have taken a look at the paper from the link you provided, in the paper, it mentions that: "This approach can also be used when there is a logical grouping of samples based on experimental conditions, and the different conditions are expected to have different variabilities." this i ...
written 13 months ago by Yanzhu Lin110
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Comment: C: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Thompson, Thank you very much for your reply and your reply is really helpful for us. I really appreciate it. We understand that DESeq/edgeR/limma-voom model the variance depending on the mean values. In addition, according to the voom paper, we also know that limma-voom can model the heterosce ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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Comment: A: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Gordon, Thank you very much for your comments. All the RNA-seq methods -- edgeR, DESeq2 and voom -- allow the variance to depend on the mean for each gene, this is exactly what I know. I will try voomWithQualityWeights() next. Thanks, Yanzhu ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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Comment: A: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... In addition, in RNAseq data analysis, we think the negative binomial model, which is used by DESeq/edgeR, can also take care of heteroscedasticity, the reason is that since variance = mean + dispersion * squared of mean, if the mean is different, then the variance will also be different. Are we corr ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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Comment: A: modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Hi Gordon, I never assume that the variances between genes are the same. What we are interested is to model the heteroscedasticity within gene, for example, in the RNA-Seq experiment, there is one factor with 5 levels and each level has several biosamples, if the variance among these 5 levels are d ...
written 13 months ago by Yanzhu Lin110 • updated 13 months ago by Gordon Smyth32k
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modeling heteroscedasticity in limma-voom for RNA-Seq data analysis
... Dear All, How would you model a factor that's heteroscedastic using limma-voom for RNA-Seq data? Best, Yanzhu ...
limma written 13 months ago by Yanzhu Lin110
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Comment: A: mixed model using limma-voom
... Hi Gordon, Thank you very much for your comments and suggestion. I have filtered the very lowly expressed genes. ...
written 13 months ago by Yanzhu Lin110

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