## User: elineverbon

elineverbon20
Reputation:
20
Status:
New User
Location:
Utrecht University, the Netherlands
Website:
http://elineverbon.com/
ElineVerbon
Last seen:
2 years, 3 months ago
Joined:
2 years, 11 months 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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... - empty post, don't know how to remove it - ...
written 2.2 years ago by elineverbon20
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... 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 2.2 years ago by elineverbon20
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... Dear Aaron, I followed up on your advice and started a new post here: https://support.bioconductor.org/p/98161/ ...
written 2.2 years ago by elineverbon20
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... 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 ...
written 2.2 years ago by elineverbon20
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... 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 2.2 years ago by elineverbon20
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... (sorry for the long messages, tried to make it as clear as possible) ...
written 2.3 years ago by elineverbon20
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... 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 2.3 years ago by elineverbon20
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... 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 2.3 years ago by elineverbon20
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... 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 2.9 years ago by elineverbon20
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... #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 2.9 years ago by elineverbon20

#### Latest awards to elineverbon

Autobiographer 2.2 years ago, has more than 80 characters in the information field of the user's profile.

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