User: swbarnes2

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swbarnes250
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Posts by swbarnes2

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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 19 days ago by swbarnes250 • updated 19 days ago by James W. MacDonald48k
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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 28 days ago by swbarnes250
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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 28 days ago by swbarnes250
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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 6 weeks ago by swbarnes250
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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 7 weeks ago by swbarnes250
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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 7 weeks ago by swbarnes250
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... The samples in your counts excerpt that you labeled "control" have the size factors associated with treat1 from colData.  Let me guess.  You made the group column by copying and modifying a command line from a tutorial, without understanding what you were doing? ...
written 8 weeks ago by swbarnes250
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Comment: C: Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
... What do you get from colData(dds)?  ​I still think you have mixed up the labeling of your samples, as those Log2Fold changes look more like treat1/treat2. ...
written 8 weeks ago by swbarnes250
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Answer: A: deseq2 analysis multiple factor and 4 different time points
... You make dds from raw counts, not normalized.  I'm not even sure what happens if you try to make a dds object with non-integer counts as input.   That method of making a concatenated "group" column is useful for comparing subsets of samples to each other, while using the dispersion of the whole da ...
written 9 weeks ago by swbarnes250
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Multiple tissue types in one DESeq2 object
... I have a project with 20 samples of one tissue, and 20 of another.  (also, there are two different genotypes, and 2 different treatments) I was wondering if I should be keeping them together as a single DEseq object if the investigators are not really interested in comparing between tissues.  I was ...
deseq2 written 11 weeks ago by swbarnes250 • updated 11 weeks ago by Michael Love20k

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