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... The answer of the question was indeed in the primary assumption of the tool itself. I should have taken that into account before going ahead. Remark 1 in particular is a very helpful general advise in this respect. Thanks a lot. solved!   ...
written 2.7 years ago by rraadd_80
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... Yes. I wanted to see whether one condition is more noisy than the other. Biological question I was trying to answer was: How much is the noise in my experiment (trt vs untrt)? what I have is 1. counts (3 replicates each for trt and untrt) and 2. a DESeq2 result (log2FoldChange, lfcSE etc.) obta ...
written 2.7 years ago by rraadd_80
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... sorry for the confusion. I am using "standard error: condition treated vs untreated" (from results columns) for the calculation. So, I meant individual calculation of variance associated with each LFC. So then the idea is to take sum of variances and divide it by square of n - which would give me ...
written 2.7 years ago by rraadd_80
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... I have a question regarding the application of standard error. To get cumulative (gene-wide) error (noise) per condition I can do following steps. I can get variance (VAR) of each gene by multiplying standard error (SE) by square root of total number of genes (n) and then squaring it.  VAR=(SE*sqr ...
written 2.7 years ago by rraadd_80
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... Thanks. I wonder if it is possible, (independent of DeSeq2) to use Wald test for negative numbers?  ...
written 3.1 years ago by rraadd_80
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... Dear users, Instead of counts (non-negative integers) required by DeSeq2, I have negative numbers and fractions, and I need to use DeSeq's statistics to find out significantly up/down genes. Since for my data, min=-10 and max=10, I can convert it into counts by  first multiplying with a consta ...
written 3.1 years ago by rraadd_80 • updated 3.1 years ago by Michael Love26k