User: elineverbon

gravatar for elineverbon
elineverbon20
Reputation:
20
Status:
New User
Location:
Utrecht University, the Netherlands
Website:
http://elineverbon.com/
Twitter:
ElineVerbon
Last seen:
2 months ago
Joined:
10 months, 3 weeks ago
Email:
e**********@gmail.com

I am a PhD candidate at Utrecht University trying to figure out the molecular response of plant roots to beneficial microbes.

Posts by elineverbon

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Adjusting for procedural effect
... - empty post, don't know how to remove it - ...
written 9 weeks ago by elineverbon20
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Answer: A: Adjusting for procedural effect
... Ah, okay. That clears things up, thank you! Thank you for making me write out the design like this. Does that mean that if I would want to correct for the sorting effect, I would have to do it by 'hand' - as in, by making a script for it myself? (As mentioned in the previous post, in that case I wo ...
written 9 weeks ago by elineverbon20
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Comment: C: Adjusting for procedural effect and deciding on statistical test
... Dear Aaron, I followed up on your advice and started a new post here: https://support.bioconductor.org/p/98161/ ...
written 9 weeks ago by elineverbon20
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Adjusting for procedural effect
... Dear, This is a follow-up on a previous question (to be found here: https://support.bioconductor.org/p/88922/#98157 ) I am trying to analyze an RNA seq dataset with EdgeR. I have 44 different samples, coming from two controls (both the full organ, namely a plant root) and five different cell types ...
edger written 9 weeks ago by elineverbon20
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Comment: C: Adjusting for procedural effect and deciding on statistical test
... Yes, you are right of course. I accidentally pasted the code that I used to remove the sorting adjustment to compare the two. In my original script I did not include the second line and did correct for the sorting. So, I used the first line for my original analysis. I added the second line (and com ...
written 9 weeks ago by elineverbon20
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Answer: A: Adjusting for procedural effect and deciding on statistical test
... (sorry for the long messages, tried to make it as clear as possible) ...
written 9 weeks ago by elineverbon20
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Answer: A: Adjusting for procedural effect and deciding on statistical test
... To correct for the sorting effect myself, I 1) took the counts per gene of the DGELists of the untreated sorted and unsorted control samples. I calculated the fold change due to sorting with EdgeR and saved this in a table. 2) divided the counts of all the sorted treated samples by the fold change ...
written 9 weeks ago by elineverbon20
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Answer: A: Adjusting for procedural effect and deciding on statistical test
... Dear Aaron Lun (and others reading along), We have continued working on this since our discussion here on the web. Here I first explain how we used your method and run into problems when trying to validate it. Next, I explain how I tried to correct for sorting myself and the problems I run into the ...
written 9 weeks ago by elineverbon20
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Comment: C: Adjusting for procedural effect and deciding on statistical test
... Design matrix:   groupCOB.sorted.NB groupCOB.sorted.WCS groupCOLsort.sorted.NB groupCOLsort.sorted.WCS groupCOLunsort.unsorted.NB 1 0 0 0 0 0 2 0 0 0 0 0 3 0 0 0 0 0 4 0 0 0 0 0 ...
written 10 months ago by elineverbon20
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Answer: A: Adjusting for procedural effect and deciding on statistical test
... #make design matrix tissue <- s2c$cell_type #s2c is a table with all the information about the samples, which the order as the order of my sequencing files sorting <- s2c$sortedness exposure <- s2c$treatment replicate <- s2c$replicate group <- factor(paste0(tissue, ".", sorting, ".", ...
written 10 months ago by elineverbon20

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