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User: casikecola

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casikecola0
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Posts by casikecola

<prev • 7 results • page 1 of 1 • next >
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Comment: C: DESeq2 LRT test behaving strangely?
... That makes sense, thanks for the clarification. I was though more concerned about the differences in-between the LRT runs (specially between 2 and 3) but I guess I am testing different things there too. My question is the effect of condition given a genotype and I would be happy to use the LRT test ...
written 4 weeks ago by casikecola0
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Comment: A: DESeq2 LRT test behaving strangely?
... Yes, you are right. I figured for 2) and 3) it would be obvious. The reduced formulas for the LRT runs were: 1. (~ genotype + condition) and (~ genotype) choosing eventually the second one 2. (~ 1) 3. (~ 1) I am using size factors computed with Scran (default settings) and the following param ...
written 4 weeks ago by casikecola0
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DESeq2 LRT test behaving strangely?
... I am using DESeq2 with single-cell data. Previously, I used the "Wald" test with default settings but I wanted to check how my previous analysis would look using the recommend single-cell settings from the vignette (basically using the "LRT" test). I have two variables and to simplify the questi ...
deseq2 written 4 weeks ago by casikecola0
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Comment: C: DESeq2 unbalanced sample size
... Thanks Michael!  ...
written 8 weeks ago by casikecola0
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DESeq2 unbalanced sample size
... My experimental design is the following: Replicate Tissue_type Genotype 1 A HE 2 A DI 3 A HE 1 B HE 2 B HE 3 B DI 4 B DI I am interested in obtained D.E. genes for the ques ...
deseq2 statistics bioinformatics bioconductor written 9 weeks ago by casikecola0 • updated 9 weeks ago by Michael Love22k
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Comment: C: DESEq2 Large Memory When Parallel
... Yes, I have come to the same conclusion. I will try with limma-voom. Thanks!  ...
written 7 months ago by casikecola0
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Comment: C: DESEq2 Large Memory When Parallel
... Hi,  My matrix has 10k rows and 1k columns. With parallel=F the memory use remains below 20GB but it takes too long to run, with parallel=T and 16 cores the memory use goes up to >300GB and with 8 cores >150GB...Is this expected?  ...
written 7 months ago by casikecola0

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