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Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
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SD filtering before DEG analysis with limma : possible or not ?
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Accounting for Batch effect reduces DEGs drastically
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Which input file is used for DGEList in EgdeR?
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Questions about the false positives indicated by DESeq2 and QQ plot
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updated 6 months ago by ▴ 10 • written 21 months ago by ▴ 10
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limma fo continous variables
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
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ranking the DeSeq2 results using t-values?
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updated 10 months ago by 41k • written 10 months ago by ▴ 10
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Batch correction and repeated measures
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updated 9 days ago by 50k • written 7 months ago by ▴ 10
1,734 results • Page 2 of 35
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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