## User: Mr.RB

Mr.RB20
Reputation:
20
Status:
New User
Location:
Last seen:
7 months, 4 weeks ago
Joined:
1 year, 7 months ago
Email:
r*******@outlook.com

#### Posts by Mr.RB

<prev • 17 results • page 1 of 2 • next >
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... I found predORF from systemPipeR to predict the longest non-overlapping reading frames in a genome, however these are the longest ORFs **per** strand. I want to have the longest ORF considering both strands, for example: AAAA**ATG**XXXXXX**TGA**AAAA CDS = XXXXXX = 6 nt <- pick this ...
written 7 months ago by Mr.RB20
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... Aaah I see. Although I don't get the statistics after the dispersion estimates (currently looking at the paper) I could imagine that the model would be like y = b0 + condition2 *b1, where b0 = mean(condition1) and b1 indicates the increase in mean for condition2.  And then test with H0: b1 == 0. How ...
written 17 months ago by Mr.RB20
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... When calculating the dispersion DESeq2 will only give one dispersion value for each gene, as can also be seen in the dispersion plot. I don't have much knowledge about statistics, but as far as I know we basically want to compare a distribution from condition 1 vs condition 2 and see whether there i ...
written 17 months ago by Mr.RB20 • updated 17 months ago by Ryan C. Thompson7.4k
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... That's why i said " the model would look like this I suppose") , but apparently I was wrong here, but then the plot I mentioned (coefficient 1 vs coefficient) does makes sense. Anyway I will re-read it ...
written 17 months ago by Mr.RB20
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... hmm I just checked it: edgeR.fit <- edgeR::glmFit(edgeR.dgelist , design) edgeR.glrt <- edgeR::glmLRT(edgeR.fit, contrast = mc) head(edgeR.fit$coefficients,2) # groupcon grouptreat #gene1 -7.057066 -7.104031 #gene2 -6.580015 -6.706760 head(edgeR.glrt$table,2) # logFC logCP ...
written 17 months ago by Mr.RB20
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... Aaah that's clear! Got all the steps now. Thankyou for the great and quick support for the questions! ...
written 17 months ago by Mr.RB20
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... Sorry for bothering you again! But I can't figure what these coefficients mean. Let's say we compare two treatments, this will result in two coefficients: the first one is the baseline for group1 and the second the 2 vs 1 comparison (according to the user guide). Indeed when I plot coefficient 1 aga ...
written 17 months ago by Mr.RB20
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... Sorry if I wasn't clear I actually ment whether I could produce a plot like the last figure on this page. Let's say I done my tag wise dispersion estimates based on the whole data, then select a single gene and its counts and dispersion. Like so: dat <- read.table(text ="con.1 con.2 treat.1 tre ...
written 17 months ago by Mr.RB20
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... Do you have any suggestions to show what a GLMfit actually does, or to explain this simply. I think the testing of coefficients would be easy understandable, but I completely forgot the fitting part... I know about the gof() plot but I think this will more focus on the results than what it actually ...
written 17 months ago by Mr.RB20
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... Thankyou! the prior.df=0 to prior.df = x should really visually clarify the compromis! ...
written 17 months ago by Mr.RB20

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