User: igor

gravatar for igor
igor30
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30
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New User
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United States
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2 weeks, 1 day ago
Joined:
4 years, 10 months ago
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i************@nyumc.org

Posts by igor

<prev • 78 results • page 1 of 8 • next >
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Comment: C: DESeq2 lfcShrink and unshrunk fold changes
... That is easy indeed. And that shouldn't break anything downstream? ...
written 29 days ago by igor30
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Comment: C: DESeq2 lfcShrink and unshrunk fold changes
... That's the option I use, but then you end up with two objects. I save the results object in case I need to access it in the future, so I was hoping to avoid having to save both of them. I could modify them, but then I am concerned there would be issues with having them in a custom format. It would g ...
written 29 days ago by igor30
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DESeq2 lfcShrink and unshrunk fold changes
... In DESeq2, it's possible to keep the unshrunk fold changes in `results()` output using `addMLE=TRUE`, but that requires `betaPrior=TRUE`. This behavior seems to be based on the old workflow. The more modern approach is to use `lfcShrink()`, but then the unshrunk fold changes are lost. Is there a wa ...
deseq2 written 4 weeks ago by igor30 • updated 29 days ago by Michael Love25k
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Comment: C: tximport discrepancy between TPMs and lengthScaledTPMs
... The problem is that I have a lot of samples that are not much better, so it's hard to define a cutoff. I also tried the more traditional STAR/featureCounts approach and had only 64k total counts. The top gene from Salmon only had 20. Clearly, there is something very odd about this sample. I would ...
written 3 months ago by igor30
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Comment: C: tximport discrepancy between TPMs and lengthScaledTPMs
... For lengthScaledTPM, only 33 with counts greater than 10. ...
written 3 months ago by igor30
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Comment: C: tximport discrepancy between TPMs and lengthScaledTPMs
... My concern was that the top gene is 67% of total by TPMs, but 98% by counts. I understand the relative increase or decrease. The part that worries me is that a single gene is soaking up nearly all of the reads. Regardless of any scaling or normalization, it's hard to reconcile all other genes essent ...
written 4 months ago by igor30
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tximport discrepancy between TPMs and lengthScaledTPMs
... I am importing Salmon output with `tximport` to get gene-level expression levels using the suggested approach: txi = tximport(quant_files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") Generally, this works as expected. However, sometimes I notice a large discrep ...
tximport written 4 months ago by igor30 • updated 4 months ago by Michael Love25k
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tximeta remote versus local reference files
... BioC 3.8 was just released and there is a great new package tximeta (at least if you work with Salmon). I am still trying to properly understand how it works. The vignette contains the following section: However, to avoid downloading remote GTF files during this vignette, we will point to a GTF fil ...
tximeta written 11 months ago by igor30 • updated 11 months ago by Michael Love25k
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... Thank you for the explanation. I should've tried more samples. Using the updated example and real samples produces reasonable results. ...
written 16 months ago by igor30
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... I tried running the example you posted. The result is close to yours: > gsva(normcounts, list(GS1=1:10, GS2=20:30), kcdf="Poisson") Sample1 Sample2 GS1 -0.148823642 0.19004598 GS2 0.002574801 0.04970183 I also tried converting to logCPM values and using the Gaussian kernel: > ...
written 16 months ago by igor30

Latest awards to igor

Popular Question 9 months ago, created a question with more than 1,000 views. For bumphunter beta values
Popular Question 13 months ago, created a question with more than 1,000 views. For DESeq2 with many samples
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DESeq2 with many samples
Popular Question 2.3 years ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 2.4 years ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 2.5 years ago, created a question with more than 1,000 views. For minfi MethylationEPIC errors
Supporter 3.7 years ago, voted at least 25 times.

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