User: n.naharfancy

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Posts by n.naharfancy

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Comment: C: log2foldchange vs density plot from likelihood and posterior
... Thank you Michael, you are right. But that will increase the number of DGEs proportionally for the standard dataset right? Which property of the dataset is driving this discrepency? How can I understand more about the dataset property? ...
written 4 weeks ago by n.naharfancy0
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Comment: C: log2foldchange vs density plot from likelihood and posterior
... Say, for this particular case of STAT3, this is a very common gene to be found upregulated under LPS treatment (ou experiment from standard sequencing and previous literature) but failed to be DE in three-prime dataset. The count for this this is not particularly low nor the fold change is very diff ...
written 4 weeks ago by n.naharfancy0
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Comment: C: log2foldchange vs density plot from likelihood and posterior
... Hi Michael, Thank you very much for commenting. I was secretly hoping that you will see my post. So, you recommend to plot bar chart with lfcSE! And, do you think this is the right comparison I am doing as to find out why these genes are not called DGEs? For example I found among 715 DGEs that w ...
written 4 weeks ago by n.naharfancy0
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Comment: C: log2foldchange vs density plot from likelihood and posterior
... ![plot using betas for standard error bar position][1] ![plot with lfc for error position][2] [1]: https://de.cyverse.org/dl/d/14669EA4-D37F-48A1-8710-F515B32AF3AE/plot.MLE.betas.png [2]: https://de.cyverse.org/dl/d/569DDDA1-4B77-4EDB-B160-8389151721CD/plot.MLE.lfc.png ...
written 4 weeks ago by n.naharfancy0
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log2foldchange vs density plot from likelihood and posterior
... Hi I am trying to visualise the spread of the mean count from MLE calculation following DEseq2, 2014 paper and the attached codes from DEseq2paper package. The difference in my case is, instead of two different genes, I am plotting the likelihood data of the same gene from two dataset. The experim ...
deseq2 written 4 weeks ago by n.naharfancy0 • updated 4 weeks ago by Michael Love24k
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Comment: C: Comparing two different sequencing method by DEseq2
... Hi Steve Thank you very much for your thought and input. I just remember, previously we have done the same experiment by sequencing the quantseq library at higher depth (~40 million) same as illumina standard but we did not see an improvement in DGEs. We only saw an increased percentage of read dup ...
written 4 weeks ago by n.naharfancy0
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Comment: C: Comparing two different sequencing method by DEseq2
... Yes, makes perfect sense, thank you. :) ...
written 4 weeks ago by n.naharfancy0
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Comment: C: Comparing two different sequencing method by DEseq2
... Hi Steve, I was also wondering if I can do something computationally to increase the DGEs number so that I have at least 85-90% overlapping? Any ideas? Also, some of the genes not called DGEs were of moderate expression. If you want to see any particular plot or data, please let me know and I can ...
written 5 weeks ago by n.naharfancy0
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Comment: C: Comparing two different sequencing method by DEseq2
... Hi Thanks for commenting. The purpose for this test was actually to see if three prime sequencing will be suitable for future experiment. So, this time the treatment was LPS, which gives over 1000 DGEs, so with three prime I got about 60% DGEs overlapping with illumina standard mRNA, but we are no ...
written 5 weeks ago by n.naharfancy0
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Comment: C: Comparing two different sequencing method by DEseq2
... Hi Steve, Thank you for taking the time to respond with such detailed answer. You are right in assuming that most of the lower count genes are not getting called significant. 1. I did analyse them completely separately to avoid wrong estimation of dispersion. I will look into `plotDispEsts`. 2. ...
written 5 weeks ago by n.naharfancy0

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