User: rrcutler

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rrcutler30
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Posts by rrcutler

<prev • 33 results • page 1 of 4 • next >
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Comment: C: DESeq2 dispersion and p-value histograms
... Hi Bernd, Thank you for the detailed reply, I have gone ahead and followed your recommendations. 2) Between time points, the estimated dispersion prior variance only differs by 0.02. However, when only loading samples relevant to a pairwise comparison of interest, there are instances where the est ...
written 16 days ago by rrcutler30
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Comment: C: DESeq2 dispersion and p-value histograms
... Hi Michael, Thanks for the response. The colors in the PCA plot represent replicates of a condition. Each cluster is representative of a different time point. I have an equal interest in all the comparisons using all samples, so is loading all in fact appropriate here? Are there any test we can do ...
written 23 days ago by rrcutler30
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DESeq2 dispersion and p-value histograms
... After reading some post that recommend checking p-value distributions after DE testing, I went back and looked at some data where the result of DE testing was 0 significantly DE genes (3 replicates, 3 conditions, 3 times). Note that this was using an experiment where all samples were loaded into DES ...
rnaseq deseq2 dispersion fdrtool written 26 days ago by rrcutler30 • updated 23 days ago by Bernd Klaus470
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Comment: C: DESeq2 Dispersion Shrinkage - more samples is better?
... Thanks for all your expertise Michael, I really appreciate it. ...
written 7 weeks ago by rrcutler30
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Comment: C: DESeq2 Dispersion Shrinkage - more samples is better?
... Hi Michael, Yes, I have read this part in the FAQ. The clustering density of the within group samples looks to be about the same across developmental stages, although the stages are clearly separated by the 2nd principle component. However, I'm still not sure why it is reasonable to use a single di ...
written 7 weeks ago by rrcutler30
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Comment: C: DESeq2 Dispersion Shrinkage - more samples is better?
... Thanks Michael, this has really helped me understand how the dispersion estimation works now in DESeq2. Knowing that mu-hat_ij is a vector incorporated with other metrics to set the mean count is a bit confusing, especially when you end up with one dispersion parameter per gene across all samples.  ...
written 8 weeks ago by rrcutler30
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Comment: C: DESeq2 Dispersion Shrinkage - more samples is better?
... Hi Michael, Since there is a single dispersion estimate per gene across the whole sample, I assume the dispersion value is plotted with the average expression of a gene across all samples. So is including more samples, in order to better estimate the dispersion, essentially just including more expr ...
written 8 weeks ago by rrcutler30
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Comment: C: DESeq2 Dispersion Shrinkage - more samples is better?
... As a side note, I have always been confused as to the relationship between the mean-dispersion and mean-SD. As you have shown in your plot, it is obvious that dispersion decreases as the mean increases. However, I have read that count data is heteroscedastic which means that the variance is greater ...
written 8 weeks ago by rrcutler30
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Comment: C: DESeq2 Dispersion Shrinkage - more samples is better?
... Hi Michael, Thanks for your helpful replies, as always.  To expand/summarize on your explanation of the mean of the dispersion prior... (please correct me if I'm wrong) Despite having small sample sizes, we want to estimate a dispersion parameter which is closest to the true population (if our num ...
written 8 weeks ago by rrcutler30
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DESeq2 Dispersion Shrinkage - more samples is better?
... Hello, Reading more on how dispersion shrinkage is working, I wanted to clarify what my understanding is as well as address a couple of questions. I have read both the DESeq2 and DDS papers that talk about dispersion shrinkage.    My understanding: The point of dispersion shrinkage is to share i ...
deseq2 dds written 8 weeks ago by rrcutler30 • updated 8 weeks ago by Michael Love15k

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