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 10 months 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 10 months 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 10 months 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 10 months 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 10 months ago by zhouqz0 • updated 10 months ago by Aaron Lun24k

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