User: Wuschel

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Wuschel10
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10
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New User
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HUJI
Last seen:
6 days, 23 hours ago
Joined:
1 year, 5 months ago
Email:
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Proteomics, Arabidopsis thaliana, gene expression, transgenic

Posts by Wuschel

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How adjusted p-values are calculated in limma
... Thank you Prof. Smyth ...
written 5 weeks ago by Wuschel10
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How adjusted p-values are calculated in limma
... 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 ...
limma statistics R fdr transcriptomics written 5 weeks ago by Wuschel10 • updated 5 weeks ago by Gordon Smyth39k
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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 3 months 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 3 months ago by Wuschel10 • updated 3 months ago by Martin Morgan ♦♦ 24k
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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 3 months 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 3 months ago by Wuschel10 • updated 3 months ago by Martin Morgan ♦♦ 24k
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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 3 months 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 7 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 7 months ago by Wuschel10 • updated 7 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 7 months ago by Wuschel10

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