User: zhouqz

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zhouqz0
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Posts by zhouqz

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Comment: C: Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2
... 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. ...
written 8 weeks ago by zhouqz0
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Comment: C: Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2
... 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 weeks ago by zhouqz0
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Comment: C: Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2
... 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?    ...
written 9 weeks ago by zhouqz0
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Comment: C: Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2
... 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 9 weeks ago by zhouqz0
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Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2CPM) of LP
... 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 ...
limma written 9 weeks ago by zhouqz0 • updated 9 weeks ago by Aaron Lun21k

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