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combat sva
•
reset
3
votes
6
replies
2.2k
views
is it necessary to check batch effect in this case? and how to?
svaseq
combat sva
RANseq
batcheffect
removebatcheffect
updated 7.5 years ago by
Jakub
▴ 50 • written 7.5 years ago by
amoltej
▴ 10
1
vote
2
replies
1.5k
views
is it possible to before and after batch effect removal from the data and see that batch effect removal actually worked
combat sva
batch effect
comba
updated 7.5 years ago by
Vegard Nygaard
▴ 110 • written 7.5 years ago by
amoltej
▴ 10
0
votes
1
reply
3.4k
views
SVA behaving weirdly, system is computationally singular , problem with method leek only
SVA
combat sva
leek
updated 2.9 years ago by
chase.mateusiak
• 0 • written 7.0 years ago by
amoltej
▴ 10
1
vote
1
reply
1.6k
views
Inspection of batch effect correction success with ComBat in R, regarding a merged dataset comprised of 4 different batches
affymetrix microarrays
sva
combat sva
batch effect
plotMDS
updated 7.7 years ago by
Jeff Leek
▴ 650 • written 7.7 years ago by
svlachavas
▴ 830
7
votes
3
replies
3.1k
views
SVA: Including variable of interest in ComBat model matrix
combat sva
SVA
sva
ComBat
batch effect
updated 8.0 years ago by
W. Evan Johnson
▴ 850 • written 8.0 years ago by
John Townsend
▴ 20
1
vote
2
replies
2.4k
views
cross platform normalization in R
R
Combat SVA
updated 8.3 years ago by
Steve Lianoglou
★ 13k • written 8.3 years ago by
nazaninhoseinkhan
• 0
0
votes
1
reply
1.2k
views
Combat prior plots good enough?
combat
combat sva
6.6 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
1
vote
2
replies
1.2k
views
Batch effect problem using SVA showing problems
SVA
combat sva
batch effect
updated 7.7 years ago by
Jeff Leek
▴ 650 • written 7.7 years ago by
amoltej
▴ 10
0
votes
0
replies
1.2k
views
removing batch effects using sva combat and linear regression
combat sva
microarry
Jeff leek
6.8 years ago
DataFanatic
▴ 10
0
votes
0
replies
628
views
Number of SVA increased after ComBat
combat sva
6.0 years ago
jonellevillar
• 0
0
votes
0
replies
818
views
Help with multiple batch effects
combat sva
batch effect
5.8 years ago
Fp
• 0
0
votes
0
replies
923
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
5.6 years ago
jmsendoya
• 0
0
votes
0
replies
1.1k
views
SVA: Using ComBat for synthetic genetic array data
combat sva
sga
combat
batch effect
8.0 years ago
John Townsend
▴ 20
0
votes
4
replies
1.8k
views
ComBat: Adjustment for 3experimental variables
ENmix
combat.mc
illumina450k
combat sva
7.8 years ago
DSP
• 0
0
votes
0
replies
920
views
SVA) Error while using 'sva' package - combat
combat sva
7.7 years ago
kkwon
• 0
0
votes
2
replies
946
views
Problem with Combat batch adjustment
combat sva
7.4 years ago
vinnu260
▴ 10
0
votes
0
replies
1.2k
views
RPKM counts with SVA package & Combat with SVA?
batch effect
combat sva
sva
7.1 years ago
Ahdee
▴ 50
0
votes
0
replies
1.2k
views
What is the input for Combat in R?
combat sva
input files
7.1 years ago
arisarkar88
▴ 40
0
votes
0
replies
886
views
SVA: Reference manual improvment
combat sva
sva
7.0 years ago
alice.anlind
• 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…
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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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