User: Wuschel
Wuschel • 10
- Reputation:
- 10
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- New User
- Location:
- HUJI
- Last seen:
- 2 weeks, 3 days ago
- Joined:
- 1 year, 2 months ago
- Email:
- y*******@gmail.com
Proteomics, Arabidopsis thaliana, gene expression, transgenic
Posts by Wuschel
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... Hi Martin, Thank you for helping with this.
This is my session info after reinstalling everything. Unfortunately Still I get this `"Error: se does not inherit from class SummarizedExperiment "`
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
...
written 19 days ago by
Wuschel • 10
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... * installing *source* package 'DEP' ...
** using staged installation
** R
Warning: no function found corresponding to methods exports from 'GenomicRanges' for: 'FactorToClass'
Warning: no function found corresponding to methods exports from 'DelayedArray' for: 'splitAsList'
* ...
written 21 days ago by
Wuschel • 10
• updated
21 days ago by
Martin Morgan ♦♦ 23k
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... DEP Steps;
# Impute missing data using the k-nearest neighbour approach (for MAR)
data_imp_knn <- impute(data_filt, fun = "knn", rowmax = 0.9)
data_diff_manual <- test_diff(data_imp_knn, type = "manual",
+ test = c('mut_0h__vs_WT_0h_ ...
written 23 days ago by
Wuschel • 10
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... Hi Arne,
This is my R details;
> version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status ...
written 23 days ago by
Wuschel • 10
• updated
23 days ago by
Martin Morgan ♦♦ 23k
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... Hi,
I am using `DEP` [package][1] for analysis of deferentially enriched proteins. I get an error when testing comparisions, this same scripts worked in my old PC.
data_diff_manual <- test_diff(data_imp_knn, type = "manual",
+ test = c('mut_0h__vs_WT_0h_', ...
written 24 days ago by
Wuschel • 10
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... Thank you very much Matthew :) ...
written 4 months ago by
Wuschel • 10
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... I would like to summarize my *Arabidopsis* proteomics data for AGIs **functional bins**.
Where can I find whole genomics functional groups?
Also, what are the pros and cons of summarizing data for the functional groups? ...
written 4 months ago by
Wuschel • 10
• updated
4 months ago by
Matthew McCormack • 180
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... Does anyone have experience in **integrating and visualizing RNASeq / Proteomics data for metabolomics pathways**?
Is there any user-friendly R package or free software available for this type of analysis?
Would be grateful if you could direct me to the right place with accessible **examples/tutor ...
written 4 months ago by
Wuschel • 10
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... Are there any methods that I can assure the quality of codes I've written?
When It comes to statistics, I always feel to double check with Excel, but feel wasting time or overthinking!
How to QC the codes? Any tips?
...
written 15 months ago by
Wuschel • 10
• updated
15 months ago by
Martin Morgan ♦♦ 23k
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