User: rrcutler

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rrcutler50
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Posts by rrcutler

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Low Counts in top DE genes in DESeq2
... Just to clarify, the reason the Wald shouldn't be used here is because there are many groups which suppresses count outliers? ...
written 15 days ago by rrcutler50
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Comment: C: Low Counts in top DE genes in DESeq2
... Hi Michael, Using the LRT I was only able to load my samples of interest (can't take advantage of dispersion shrinkage). The results of using a LRT with the same comparison in my first post has 1598 DE genes while the first only had 385 DE genes. Although, glancing over the count values, the LRT te ...
written 17 days ago by rrcutler50
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Low Counts in top DE genes in DESeq2
...  Hello all, I am experiencing strange results from the output of DESeq2. I am getting many genes that have low counts in the conditions I am comparing. This is one striking example where a gene that is significantly differentially expressed has 0 counts in both conditions! I have also seen cases wh ...
deseq2 written 23 days ago by rrcutler50 • updated 23 days ago by Michael Love16k
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Comment: C: Use interactions to get the difference in the effect of two treatments
... Hi Michael,  Yes, the columns of counts are indeed identical. Your equation makes this situation clear. So in order to find the difference in effect between the conditions, the comparison of two conditions to the control is actually the same as the direct comparison of the conditions to each other? ...
written 4 weeks ago by rrcutler50
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Use interactions to get the difference in the effect of two treatments
... Hello all, I have two experimental conditions and one control, I want to compare the difference of these effects in reference to the control. A simple way to do this would to get the gene sets that result from comparing each experimental level to the control separately, and then take the difference ...
deseq2 written 5 weeks ago by rrcutler50 • updated 5 weeks ago by Michael Love16k
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Answer: A: fdrtool - How does it work?
... For anyone else who is looking, I found this post helpful: https://support.bioconductor.org/p/71438/ From my own analysis to gain an intuitive understanding of what fdrtool is doing when it is re-estimating the null model for a right-skewed p-value distribution (overestimation of dispersion), I com ...
written 9 weeks ago by rrcutler50
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Comment: C: DESeq2: How to find out how well the model fits the data?
... This answer is not helpful at all. There is no where in these manuals that tells us how well the model fits the data ...
written 9 weeks ago by rrcutler50
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fdrtool - How does it work?
... Hello all,   I have been working with the "fdrtool" lately, but am having trouble understanding how it works on an intuitive level. Specifically, I have been using it with non-uniform p-value distributions in order to estimate the variance of the model using the z-scores from wald tests (DESeq2).  ...
deseq2 fdrtool written 10 weeks ago by rrcutler50
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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 3 months ago by rrcutler50
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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 3 months ago by rrcutler50

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