User: igor

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igor20
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United States
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2 months ago
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4 years, 8 months ago
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Posts by igor

<prev • 75 results • page 1 of 8 • next >
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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 9 weeks ago by igor20
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Comment: C: tximport discrepancy between TPMs and lengthScaledTPMs
... For lengthScaledTPM, only 33 with counts greater than 10. ...
written 9 weeks ago by igor20
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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 9 weeks ago by igor20
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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 9 weeks ago by igor20 • updated 9 weeks ago by Michael Love24k
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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 9 months ago by igor20 • updated 9 months ago by Michael Love24k
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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 14 months ago by igor20
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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 14 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... Thank you for clarifying. Would I also need to length-normalize (convert to TPMs/FPKMs) if I use the Gaussian kernel? Or would normalized counts be appropriate? ...
written 14 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... There is a recent related thread on the GenePattern forum: You can run ssGSEA using RNA-Seq data. This would generally work if your samples raw counts are not too different from one another. If counts vary too much, you may consider normalizing your data (e.g., so that they are between 0 and 1). Ad ...
written 14 months ago by igor20
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Comment: C: Pre-processing RNA-seq data (normalization and transformation) for GSVA
... When you say "integer counts", do you mean that they have to be the raw counts or can they be normalized counts (wouldn't be integers)? ...
written 14 months ago by igor20

Latest awards to igor

Popular Question 7 months ago, created a question with more than 1,000 views. For bumphunter beta values
Popular Question 12 months ago, created a question with more than 1,000 views. For DESeq2 with many samples
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DiffBind differential binding normalization with different levels of binding
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 with many samples
Popular Question 2.2 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 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 minfi MethylationEPIC errors
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