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DESeq
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1
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2
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304
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evaluate the variable importance on genes
DESeq2
deseq
9 weeks ago
Meme
• 0
0
votes
2
replies
329
views
Running DESeq on normalized data
deseq
DESeq2
updated 4 months ago by
ATpoint
★ 4.0k • written 4 months ago by
Hugo
• 0
2
votes
2
replies
512
views
Predicting missing values splines DESeq2
deseq
DESeq2
5 months ago
georgii.vdovin
• 0
0
votes
1
reply
372
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 5 months ago by
Michael Love
41k • written 5 months ago by
georgii.vdovin
• 0
0
votes
1
reply
642
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
khaserdene99
• 0
0
votes
3
replies
870
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
Abir.khazaal
▴ 10
0
votes
4
replies
634
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Ndimensional
▴ 20
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 8 months ago by
Erika
• 0 • written 9.2 years ago by
c.lieftink@nki.nl
▴ 40
8 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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