User: asd

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asd0
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Posts by asd

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Comment: C: DESeq2 for single gene
... If I have ~60k gene and filter the matrix to contain just 10 gene and after that I run DESeq(dds). Does the filtering affect the result of the method? To clarify the original question: I assume that one gene in my count dataset has different distribution if I consider given cases. I would have like ...
written 6 months ago by asd0
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DESeq2 for single gene
... I have 950 cases and ~60k genes in a matrix and I would like to test differential expression for one gene.  The conditions are true only for that gene. If the countData parameter of DESeqDataSetFromMatrix  function has a matrix only with one row, it doesnt work. How can I do it? ...
rnaseq deseq2 written 6 months ago by asd0 • updated 6 months ago by Michael Love14k
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Comment: C: DESeq2 incorrect basemean
... Why does the summary show that I have no outlier? out of 4 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 0, 0% LFC < 0 (down) : 3, 75% outliers [1] : 0, 0% low counts [2] : 0, 0% (mean count < 1) ...
written 6 months ago by asd0
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Comment: C: DESeq2 incorrect basemean
... Thank you for your answer. How can I calculate the base mean per level with replaced extreme count outliers? ...
written 6 months ago by asd0
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DESeq2 incorrect basemean
... I have four genes in four rows in a matrix. The results function of the DESeq2 calculated the baseMean of the four row as 37.6, 2071.5, 1.0, 491.6 But if I calculate the means with rowMeans(counts(dds,normalized=TRUE)), then I get 45.2, 2679.8, 1.0, 491.6 Why is this happen? And when I calcul ...
deseq2 mean written 6 months ago by asd0 • updated 6 months ago by Michael Love14k

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