User: rraadd_8
rraadd_8 • 0
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Posts by rraadd_8
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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!
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written 16 months ago by
rraadd_8 • 0
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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 16 months ago by
rraadd_8 • 0
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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 16 months ago by
rraadd_8 • 0
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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 16 months ago by
rraadd_8 • 0
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... Thanks. I wonder if it is possible, (independent of DeSeq2) to use Wald test for negative numbers?
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written 21 months ago by
rraadd_8 • 0
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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 21 months ago by
rraadd_8 • 0
• updated 21 months ago by
Michael Love ♦ 19k
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