User: aec

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aec30
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Posts by aec

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Comment: C: weird behaviour DESeq2 1.18.1
... Thanks a lot for the appropriate reply Michael. ...
written 6 weeks ago by aec30
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Comment: C: weird behaviour DESeq2 1.18.1
... Michael, these are normalized counts (scale="row"). What happens here is that I have three different groups and I have to perform pairwise comparisons and I run the DESEq2 just once and extract the desired comparisons. Your filter only works if I run DESeq2 every time for the desired comparison. Eac ...
written 6 weeks ago by aec30
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Comment: C: weird behaviour DESeq2 1.18.1
... Michael, it is what I did and the filtering did not solve the problem ( I have explained it above). ...
written 6 weeks ago by aec30
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weird behaviour DESeq2 1.18.1
... Dear all, Since I am using DESeq2 version 1.18.1 I observe a weird behaviour with the significant genes. As you can see on the heatmap below, the top 50 most significant genes are plotted (FDR<5%) and it is full of outliers. I am running DESeq2 with default options. I also tried to pre-filter th ...
deseq2 outliers version written 6 weeks ago by aec30 • updated 6 weeks ago by Michael Love17k
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Comment: C: significant genes with DESeq2 plenty of outliers and zero counts
... Yes, the above code helped me, but still, I do not understand why DESeq2 is not able to deal with these cases with default options. ...
written 10 weeks ago by aec30
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Comment: C: significant genes with DESeq2 plenty of outliers and zero counts
... Hi Michael, I have 20 samples, 10 per group ( I think DEseq2 requires minimum of 7 for outliers). and the normalized counts of 2 significant genes:    s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 ...
written 10 weeks ago by aec30
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significant genes with DESeq2 plenty of outliers and zero counts
... Dear all, I run DESeq2_1.18.1 with default options and obtained odd results. The significant transcripts (FDR<5%) are due to one or two outlier samples. I checked the expression values and all samples except the outliers have 0 counts, How can I deal with this situation? Which parameters shoul ...
deseq2 outliers zero counts odd results written 10 weeks ago by aec30 • updated 10 weeks ago by Michael Love17k
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Comment: C: disagreement between log2FoldChange and lfcMLE in DESeq2
... Mike I am using version DESeq2_1.10.1, is it too old? ...
written 4 months ago by aec30
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disagreement between log2FoldChange and lfcMLE in DESeq2
... Dear all, I am using DESeq2 for a design ~PAIR+GROUP and I obtained for geneX this result:     geneX baseMean 62.2087194 log2FoldChange -0.33167142 lfcMLE -2.32040851 lfcSE 0.07892334 stat -4.20245054 pvalue 2.64E ...
deseq2 log2fc shrinkage written 4 months ago by aec30 • updated 4 months ago by Michael Love17k
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question about "write.fit" function in limma-voom
... Dear all, Anybody knows how to extract the write.fit table with method="nestedF" ? the function only gives option for method="separate" or "global". Thanks, ...
limma write.fit method nestedf written 6 months ago by aec30

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