User: moushengxu

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moushengxu290
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Posts by moushengxu

<prev • 180 results • page 1 of 18 • next >
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Comment: C: heatmap.2 has become very slow in plotting heatmap.
... This worked for me like a charm: remove.packages('gplots'); library('devtools'); install_github("ChristophH/gplots") ...
written 5 days ago by moushengxu290
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Comment: C: mixing R ggplot2 with old style plot
... Tried what you suggested and various other combinations without luck. Taking a break. Really wish R were OO-R. :) ...
written 18 days ago by moushengxu290
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Comment: C: mixing R ggplot2 with old style plot
... "text(..)" works, but it just that the labels could jumble together. Not sure if gridBase has the same problem. The reason I want to use "ggrepel" is that it can automatically label data points without overlaying the text on each other. ...
written 18 days ago by moushengxu290
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mixing R ggplot2 with old style plot
... I am trying to automatically label some of the data points on a manhattan plot. For those who do not know what a manhattan plot is, it really does not matter. Rewriting the old style R code in ggplot2 seems to be a bigger challenging for me. Since the only feature I want to add to the script is to b ...
software error R snp written 18 days ago by moushengxu290 • updated 18 days ago by dariober8.4k
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Comment: C: Enrichment Analysis from DESeq2 data
... log2FC is not stable, lower p-value is more stable. I would weigh true signal more than big signal. My personal experience also supports this view. Actually, ranking by -log(P-value) * sign(logFC) is identical to ranking by signal-to-noise ratio. ...
written 19 days ago by moushengxu290
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edgeR and contrast
... Suppose you have 5 experimental conditions: no treatment control, compound A treatment, compound B treatment, compound A + B treatment, compound A_covalently_linked_to_B treatment. Or simply: control, A, B, A+B, A_B. All compounds are at the same concentration, e.g., 1uM. Your job is to compare A_B ...
R next-gen rna-seq written 4 weeks ago by moushengxu290
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Comment: C: edgeR analysis dilemma -- what samples to include
... Agreed. A related technical question: on the heatmap, can you cluster genes by the DEG between C & A and let B tag along without B being involved in the gene clustering? It would be nice if this can be done. ...
written 6 weeks ago by moushengxu290
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Comment: C: edgeR analysis dilemma -- what samples to include
... Yeah, sounds reasonable to me. One thing worth mentioning might be the heatmap. Most biologists still think pair-wisely. When you present your heatmap, probably a better way is to just show (c1,c2,a1,a2) or (c1,c2,b1,b2) for your top hits. (c1,c2,a1,a2,b1,b2) can be shown if you display all genes or ...
written 6 weeks ago by moushengxu290
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Comment: C: edgeR analysis dilemma -- what samples to include
... Well said. Thanks much! ...
written 6 weeks ago by moushengxu290
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Comment: C: edgeR analysis dilemma -- what samples to include
... Thought similarly. Would you have a better estimation of variance if you have more samples? ...
written 6 weeks ago by moushengxu290

Latest awards to moushengxu

Popular Question 5 weeks ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Scholar 11 weeks ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Popular Question 4 months ago, created a question with more than 1,000 views. For t-test or linear regression?
Popular Question 4 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation
Popular Question 8 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Supporter 9 months ago, voted at least 25 times.
Centurion 10 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Scholar 15 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Rising Star 15 months ago, created 50 posts within first three months of joining.

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