User: Wuschel

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Wuschel10
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New User
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HUJI
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2 weeks, 3 days ago
Joined:
1 year, 2 months ago
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Proteomics, Arabidopsis thaliana, gene expression, transgenic

Posts by Wuschel

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Error: se does not inherit from class SummarizedExperiment
... 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 Wuschel10
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Comment: C: Error: se does not inherit from class SummarizedExperiment
... * 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 Wuschel10 • updated 21 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Error: se does not inherit from class SummarizedExperiment
... 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 Wuschel10
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Comment: C: Error: se does not inherit from class SummarizedExperiment
... 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 Wuschel10 • updated 23 days ago by Martin Morgan ♦♦ 23k
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Error: se does not inherit from class SummarizedExperiment
... 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_', ...
summarizedexperiment dep written 24 days ago by Wuschel10
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Comment: C: Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
... Thank you very much Matthew :) ...
written 4 months ago by Wuschel10
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Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
... 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? ...
proteomics R rna-seq written 4 months ago by Wuschel10 • updated 4 months ago by Matthew McCormack180
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How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
... 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 ...
metabolomics proteomics R kegg transcriptomics written 4 months ago by Wuschel10
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How can I check the quality of code I have written? How to QC?
... 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? ...
limma R bioconductor written 15 months ago by Wuschel10 • updated 15 months ago by Martin Morgan ♦♦ 23k

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