User: tg369

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tg36940
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Posts by tg369

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Agilent description of headers
... You should use gBGSubSignal i.e. the background subtracted signal intensity.  Also if a probe is detected (above background) then gIsWellAboveBG should be greater than zero.   ...
written 6 weeks ago by tg36940
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co-evolution analysis for RNA
... I want to analyse co-evolution of a non-coding RNA with a protein coding RNA. Please anyone can advice me how to proceed? R-package and literature? Many thanks in advance for consideration.      ...
genetics written 6 weeks ago by tg36940
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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 11 months ago by tg36940
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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 11 months ago by tg36940
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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 11 months ago by tg36940

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Identify up and down regulated genes in affymetrix data

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