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DE analysis
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4
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Why does the filtering of lowly expressed genes for analysis with edgeR must be done unsupervised?
edgeR
RNAseq
DE analysis
gene filtering
7.8 years ago • updated 7.7 years ago
Mau
▴ 50
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 5 months ago by
georgersmith
• 0 • written 4.7 years ago by
lim6432
▴ 50
2
votes
7
replies
2.4k
views
About differentially expressed genes that found by edgeR
edgeR
DE analysis
fold change
cpm
updated 7.7 years ago by
Ryan C. Thompson
★ 7.9k • written 7.7 years ago by
Sara
▴ 10
1
vote
8
replies
1.9k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq
DESeq2
outlier
counts
DE analysis
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
DcL-A
• 0
0
votes
3
replies
1.5k
views
Is the CPM filtering method from NOISeq unsupervised?
rnaseq
de analysis
gene filtering
noiseq
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
Mau
▴ 50
0
votes
1
reply
924
views
miR DE analysis using DeSeq2
DE analysis
miR
deseq2
mirplant
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
weissert
• 0
6 results • Page
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Replies
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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