User: rraadd_8

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rraadd_8 • 0
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Posts by rraadd_8

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Comment: C: standard error value (lfcSE) returned by DeSeq2
... 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_8 • 0
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Comment: C: standard error value (lfcSE) returned by DeSeq2
... 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_8 • 0
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Comment: C: standard error value (lfcSE) returned by DeSeq2
... 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_8 • 0
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Comment: A: standard error value (lfcSE) returned by DeSeq2
... 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_8 • 0
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Comment: C: DeSeq2: Use negative numbers and fractions
... Thanks. I wonder if it is possible, (independent of DeSeq2) to use Wald test for negative numbers?  ...
written 3.1 years ago by rraadd_8 • 0
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DeSeq2: Use negative numbers and fractions
... 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 ...
deseq2 logfoldchange written 3.1 years ago by rraadd_8 • 0 • updated 3.1 years ago by Michael Love ♦ 26k

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