User: Wox
Wox • 440
- Reputation:
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Posts by Wox
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... Hi Devon, just curious to know, in DEG, what do you mean by between groups?
If I have a time-course experiment (3-time points) with several genotypes (WT vs 3 different mutants); and my pairwise comparison is mut vs WT at its time point (e.g. 'mut1_0h-WT_0h', mut2_0h-WT_0h', etc),
What does mean by ...
written 3 days ago by
Wox • 440
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124
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... Hi @rpolicastro this is my own analysis based on this data analysis pipeline
This experiment has
3 time points - 0 h/12h /24 hrs
4 genotypes - WT, 3 mutants (aox1/ aox2/ aox3)
https://github.com/wyguo/ThreeDRNAseq/blob/master/vignettes/user_manuals/3D_RNA-seq_command_line_user_manual.md
#Speci ...
written 3 days ago by
Wox • 440
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1
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428
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... Thank you very much :) ...
written 7 months ago by
Wox • 440
6
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1
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428
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7 follow
1
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... In Gene ontology and KEGG analysis, Why there are two cutoff values; p-value and (-) log10(FDR) value?
What is the role of these two cut-offs?
Could bioinformatician give an explanation to a wet lab person?
...
written 7 months ago by
Wox • 440
• updated
7 months ago by
jared.andrews07 ♦ 8.6k
3
votes
0
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212
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5 follow
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... What are the possible ways that I could compare two Gene interaction Networks?
WT upregulated genes interaction network vs `Mutants upregulated genes interaction network` ...
written 9 months ago by
Wox • 440
0
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1
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1
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... Thank you very much, Prof. Hope you are keeping well. Stay safe and Blessed in this current situation :) ...
written 11 months ago by
Wox • 440
3
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1
answer
1.1k
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1
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... What is the meaning of **(-) log10(FDR)** value
How to interpret higher negative value to lower negative value by comparing each other?
e.g. 1:
Ribosome : *(-) log10(FDR) = 25*
Golgi : *(-) log10(FDR) = 5*
e.g. 2:
[![enter image description here][1]][1]
[1]: https://i.stack.imgur.com/zCAMa. ...
written 11 months ago by
Wox • 440
• updated
11 months ago by
Istvan Albert ♦♦ 86k
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453
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... Not for the top-level, Just after normalizing & Imputation steps! ...
written 11 months ago by
Wox • 440
0
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0
answers
453
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0
answers
... Thank you, Just want to learn how to export data to csv files and working with dplyr. ...
written 11 months ago by
Wox • 440
2
votes
0
answers
453
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0
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... Could you help me to find Intuitive Introductory resources to `bioconductor expressionset` and `summarizedexperiment` and learn how to work with SE data (At the end wanna handle edgeR, DEP, limma, and DESEQ2 packages by myself)
Any gentle introduction? It seems difficult to get familiar with these ...
written 12 months ago by
Wox • 440
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For HeatMap: how to cluster only the rows and keep order of the heatmap's column labels as same as in the df?
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For How to use tidyr package to average replicate data for different time points and plot each gene separately?
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