User: tg369

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tg36930
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Posts by tg369

<prev • 3 results • page 1 of 1 • next >
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Answer: A: Identify up and down regulated genes in affymetrix data
... I generally draw a volcano plot to see where I can put threshold for adjusted pvalue and logFC. I most cases I use padj<0.05 and logFC>=0.58 (i.e. 1.5 fold up) or logFC<=-0.58 (i.e. 1.5 fold down) to identify differentially expressed genes. However, where you can put threshold to the logFC ...
written 3 months ago by tg36930
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Answer: A: Sparsity plot and how that indicates a model fit to negative binomial distributi
... thank you Michael for this helpful explanation. ...
written 3 months ago by tg36930
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Sparsity plot and how that indicates a model fit to negative binomial distribution
... I learn from DESeq2 that sparsity plot can provide insight regarding a data fit to negative binomial.  Running my RNA seq data (3 controls and 3 tests) in DESeq2 and then generating sparsity plot using plotSparsity(), I got a graph (https://www.dropbox.com/sh/bj12eelleqzehzx/AAD8MHoNIRhueXTdWyyl_c ...
deseq2 written 3 months ago by tg36930

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