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5
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4
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DESeq2 with multiple variable give me different results
Factor
Levels
Dispersionestimates
DESeq2
2.5 years ago
rafaelsolersanblas
▴ 50
3
votes
11
replies
3.4k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 6.8 years ago by
Peter Langfelder
★ 3.0k • written 6.8 years ago by
sup230
▴ 30
2
votes
3
replies
1.6k
views
GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
genomicranges
RaggedExperiment
coercion
logical
factor
updated 6.4 years ago by
Marcel Ramos
690 • written 6.4 years ago by
Taran
• 0
2
votes
2
replies
1.4k
views
How to extract factor levels of coldata from deseq object?
deseq2
levels
factor
colData
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
ariel
▴ 20
0
votes
2
replies
1.8k
views
GenomicRanges: `seqnames<-` can not work as expected
genomicranges
seqnames
factor
7.5 years ago
wcstcyx
▴ 30
0
votes
1
reply
662
views
DESeq2: Difference between two groups of conditions
factor
DESeq2
MultipleComparison
updated 2.4 years ago by
swbarnes2
★ 1.3k • written 2.4 years ago by
diegocastano182
• 0
0
votes
0
replies
815
views
Package in R to determine which factor values are overrepresented within a particular factor of interest
R
overrrepresentation
factor
variable
factor enrichment
7.5 years ago
IOM
▴ 20
7 results • Page
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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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