User: rrcutler

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rrcutler50
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Posts by rrcutler

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Convert Normalized RNA-Seq counts to TPM after Batch Correction
... Hi Michael, I think you forgot the links you were mentioning. -R ...
written 13 days ago by rrcutler50
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Comment: C: Convert Normalized RNA-Seq counts to TPM after Batch Correction
... Hi Michael, Thanks for you reply, I'll try your first suggestion. Could you expand on why TPM is not a great normalization? I am providing the batch to `mod` as I just have a single group of the same condition where I wish to remove the batch in between them. Is there a better way of using SVA for ...
written 15 days ago by rrcutler50
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Convert Normalized RNA-Seq counts to TPM after Batch Correction
... Hello all, I have performed batch correction using SVA using normalized counts generated from DESeq2. I then used a function in Limma in order to adjust log normalized counts in so that I can output these batch corrected counts to do analysis that does not involve differential expression. Now I hav ...
limma sva deseq2 written 16 days ago by rrcutler50
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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 11 weeks 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 11 weeks 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 12 weeks ago by rrcutler50 • updated 12 weeks ago by Michael Love17k
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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 3 months 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 3 months ago by rrcutler50 • updated 3 months ago by Michael Love17k
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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 4 months 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 4 months ago by rrcutler50

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