User: Wuschel
Wuschel • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- HUJI
- Last seen:
- 6 days, 23 hours ago
- Joined:
- 1 year, 5 months ago
- Email:
- y*******@gmail.com
Proteomics, Arabidopsis thaliana, gene expression, transgenic
Posts by Wuschel
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... Thank you Prof. Smyth ...
written 5 weeks ago by
Wuschel • 10
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... During the p.adj , many measurements (different genes) from the same sample (i.e one column of the image)
does it take all the p values from across all the samples and rank them? or ranking gene by gene and calculate the p.adj?
For example, if we have 100 genes that we want to test for difference ...
written 5 weeks ago by
Wuschel • 10
• updated
5 weeks ago by
Gordon Smyth ♦ 39k
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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 3 months 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 3 months ago by
Wuschel • 10
• updated
3 months ago by
Martin Morgan ♦♦ 24k
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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 3 months 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 3 months ago by
Wuschel • 10
• updated
3 months ago by
Martin Morgan ♦♦ 24k
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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 3 months ago by
Wuschel • 10
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... Thank you very much Matthew :) ...
written 7 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 7 months ago by
Wuschel • 10
• updated
7 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 7 months ago by
Wuschel • 10
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