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User: swbarnes2

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swbarnes270
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Posts by swbarnes2

<prev • 29 results • page 1 of 3 • next >
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Answer: A: Appropriate design formula for DESeq2 from principles
... AFAIK, the ordering of terms doesn't matter if you specify the contrast you desire in your results statement. ...
written 10 days ago by swbarnes270
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Answer: A: How to find Top 10 expressed genes in DESeq2
... This will give you the genes with the highest number of counts, but for some library preps, count numbers for a gene can be related to the length of the transcript, so you would want to correct for that if it was a factor with your library prep. ...
written 18 days ago by swbarnes270
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Answer: A: Remove any rows with 0 count in S4
... rowCounts? I think you want dds <-dds[rowSums(counts(dds)) > 1,] ...
written 22 days ago by swbarnes270
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Comment: A: Differential expression analysis error
... Cross-posted https://www.biostars.org/p/361419/ ...
written 22 days ago by swbarnes270 • updated 22 days ago by Gordon Smyth36k
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DESeq2 on mixed species samples
... I have a set of RNAseq data for 24 samples, half of them human culture, half of them human mixed with mouse.  (Also, three replicates each with 4 treatments) For the mixed ones, about 50% of the counts map to mouse genes.  I don't believe the submitters care about what's going on in the mouse genes. ...
deseq2 written 12 weeks ago by swbarnes270 • updated 12 weeks ago by James W. MacDonald49k
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Answer: A: What is colData? How do I make one?
... Since you are new, I strongly recommend that you find a tutorial with example data, and walk through the tutorial with it, stopping to examine what you've got every step, so you understand what's going on.  Walk through a few different tutorials, with their data and with yours. But yes, you need co ...
written 3 months ago by swbarnes270
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Comment: C: importing Tximport to DESeq2 for a time series experiment
... Why is your condition in hours, and not "light"? ...
written 3 months ago by swbarnes270
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Answer: A: DESeq2 Multi-Sample Test
... For starters, I'd do PCA as shown in the vignette, see if sex and day really matter much.  Day of RNA extraction and day of library prep very well might matter, but if those are the same, day of sequencing run probably won't matter.  But after that, to specifically compare one group to another, use ...
written 3 months ago by swbarnes270
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Comment: C: Differentiating between batch and treatment effects in edgeR, DESeq2
... It helps that the RNA was extracted on the same day, though it would be better if the libraries had been prepped on the same day as well.  Different run dates on the instrument is not likely to be a large source of variation if everything else happened at the same time.  So resequencing the same lib ...
written 4 months ago by swbarnes270
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Answer: A: DESeq2 memory allocation question
... The simple solution is to make your matrix smaller, by getting rid of genes that are unlikely to be interesting, either because their counts are too low to be reliable, or because they don't vary much across samples.     dds <-dds[rowSums(counts(dds)) > whateverFilterNumber,]   Is a dead ...
written 4 months ago by swbarnes270

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