User: dpc
dpc • 160
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Posts by dpc
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... Hi, I am doing differential abundance analysis and finding out biomarker from gut metagenomic sequences. For biomarker analysis, I am using the LefSe tool which has a default LDA score of 2.00. Can I lower this cut-off and still can consider significantly different taxa as a biomarker? If yes, which ...
written 7 weeks ago by
dpc • 160
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... Thanks zorbax. The default LDA value has kept as 2.00 in LefSe. Can you please suggest the minimum LDA score I can consider to find biomarker by LefSe analysis?
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written 7 weeks ago by
dpc • 160
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... Hi - I have a basic question regarding the tool `LefSe` which is used for biomarker discovery. What I understand so far is, this tool at first does a Kruskal-Wallis test between groups followed by Wilcoxon rank-sum test among the subgroups. So far, so good. At last, it calculates the **` Effect Size ...
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... I have around 52 files named like: `ERR260147.genefamilies.tsv`, `ERR260158.genefamilies.tsv` `ERR275198.genefamilies.tsv`, etc and each file has two columns. I want to change the second column name of each file according to the name of the file. For example, the second column name for file `ERR2601 ...
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... Thanks Kevin for your suggestion and help. I will definitely take a look on it and let you know. Actually I want only the stars to be reflected inside the cells of the heatmap, not the values. I want this because I have a correlation heatmap of 150 microbes X 150 microbes it is quite large and the c ...
written 5 months ago by
dpc • 160
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... Thanks Antonio. I am deleting the question here. I have posted it as a new question [here][1] . I will like to draw your attention to the query.
Thanks,
dpc
[1]: https://www.biostars.org/p/464247/ ...
written 5 months ago by
dpc • 160
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... Hi there!!! I want help regarding the correlation heatmap generation showing the significance level within the heatmap cells. I want to show the P-value <0.05 as "*" and P-value <0.001 as "**".
For that, I am following the script from [here][1]. You can find the script under the header "Star ...
written 5 months ago by
dpc • 160
• updated
5 months ago by
Kevin Blighe ♦ 71k
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... Hi there!!! I am using pheatmap package to generate heatmap from correlation value. I want to show the significance level as '*' (P value < 0.05) and '**' (P value <0.01) within the cells. How can I do that? Can anyone please help?
Thanks,
DC7
...
written 5 months ago by
dpc • 160
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... Thanks, Antonio. Yes, I have already used it. I asked just to have a cross-check my data with another method if available. ...
written 5 months ago by
dpc • 160
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... Do you have any idea how can I find out (statistically) the differentially abundant taxa from metaphlan output? ...
written 5 months ago by
dpc • 160
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