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cydar
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Comparison of cydar to other Bioconductor packages for flow cytometry analysis
cydar
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
thkapell
▴ 10
1
vote
6
replies
1.6k
views
Re: Cydar. Can I Normalize CyTOF data with just one FCS file/batch and if so, which normalization mode is recommended?
Cydar
CyTOF
normalization
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
ghogg
• 0
0
votes
4
replies
1.1k
views
Using output from normalizeBatch() outside of cydar package
cydar
mass cytometry
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
kenneth.baker
• 0
2
votes
8
replies
1.5k
views
Cydar normalizeBatch specifying batches
Cydar
normalization
normalizeBatch
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Florent
▴ 10
2
votes
4
replies
911
views
Cydar's countCells tolerance parameter for arcsinh-transformed data
cydar
CyTOF
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
mikhael.manurung
▴ 270
1
vote
2
replies
811
views
cydar: negative values for cell assignment indices
cydar
6.8 years ago
Lukas Weber
• 0
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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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