User: zhouqz
zhouqz • 0
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Posts by zhouqz
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... I just want to know why base on the definition of logFC. You and Gordon are right. the actual logFC is base on the coefficient. Thanks again.
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written 8 days ago by
zhouqz • 0
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... I manually remove the batch effect with weights base on the function of removeBatchEffect. However, the result still does not match to the autal logFC of topTable.
rv <- voom(x, design, plot=FALSE)
design.BatchEffect=model.matrix(~0+group)
batch <- as.factor(x$samples$lane)
contrasts(batch) ...
written 9 days ago by
zhouqz • 0
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... Dear Gordon,
Thank you very much for your reply. I have removed the batch effect, but the subtraction of means still does not matches the actual logFC. I have displayed the test code. Is it ok?
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written 10 days ago by
zhouqz • 0
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... Dear Aaron,
Thank you very much for your answer. I saw the code of lm.wfit. I can get the coefficient base on the v$E and v$weight. But I do not know how to get the final expression for each sample matching to logFC of topTable. In Law et al(2016) paper, the v$E was considered as the final express ...
written 10 days ago by
zhouqz • 0
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... I am confused about the log2FC when I use the limma to analyze the RNA-seq data. In the paper (Law et al. 2016; https://f1000research.com/articles/5-1408 ), Log2FC of the gene (ENTREZID:12759) is -5.44 in basal.vs.lp, getting from topTable (Page 15). However, the mean expression getting from voom ...
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