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GENESIS
•
reset
0
votes
1
reply
113
views
Reference categories for factors
assocTestSingle
GENESIS
written 3 months ago by
SuperD
• 0
0
votes
2
replies
265
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix
GENESIS
Plants
7 months ago
Monica
• 0
1
vote
2
replies
2.9k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 2.3 years ago by
Anna
• 0 • written 3.5 years ago by
solanum
• 0
0
votes
1
reply
504
views
Approximations to Est and Est.SE in GENESIS
GENESIS
2.5 years ago
Stephanie M. Gogarten
▴ 840
0
votes
0
replies
411
views
X chromosome analyses for males in GENESIS
GENESIS
2.6 years ago
Stephanie M. Gogarten
▴ 840
0
votes
3
replies
864
views
Alternate allele for GENESIS?
genesis
effect allele
association analysis
updated 2.8 years ago by
Stephanie M. Gogarten
▴ 840 • written 2.8 years ago by
ucbtapc
• 0
0
votes
1
reply
463
views
using GENESIS R package with non-human species
genesis
gwastools
2.9 years ago
Stephanie M. Gogarten
▴ 840
0
votes
2
replies
566
views
Association testing model in GENESIS
genesis
updated 2.9 years ago by
Stephanie M. Gogarten
▴ 840 • written 2.9 years ago by
o.giannakopoulou
• 0
0
votes
1
reply
672
views
GENESIS multiple gds files
genesis
gds
SeqVarData
updated 3.0 years ago by
Stephanie M. Gogarten
▴ 840 • written 3.0 years ago by
JT
• 0
0
votes
8
replies
979
views
Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
3.3 years ago
alipka
▴ 10
2
votes
1
reply
420
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 3.3 years ago by
Stephanie M. Gogarten
▴ 840 • written 3.3 years ago by
lassana.a.samarakoon
▴ 10
0
votes
0
replies
607
views
Normalisation of Data before loading in TMixClust
rna-seq
tmixclust
k-means clustering
gene expression
genesis
3.5 years ago
astridite
• 0
2
votes
1
reply
528
views
Why did the Wald test disappear from GENESIS?
genesis
3.6 years ago
Stephanie M. Gogarten
▴ 840
1
vote
3
replies
948
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
3.6 years ago
Corey.Cox
• 0
1
vote
1
reply
673
views
Calculating the z score from wald test association results in GENESIS
GENESIS
zscore
wald
updated 3.6 years ago by
Stephanie M. Gogarten
▴ 840 • written 3.7 years ago by
lassana.a.samarakoon
▴ 10
3
votes
6
replies
909
views
Interpreting the output of score test using GENESIS
genesis
output
score
updated 3.7 years ago by
Stephanie M. Gogarten
▴ 840 • written 3.7 years ago by
lassana.a.samarakoon
▴ 10
2
votes
4
replies
654
views
Sporadic missingness with admixmmap
genesis
admixmap
updated 3.7 years ago by
Stephanie M. Gogarten
▴ 840 • written 3.7 years ago by
GENOMIC_region
• 0
0
votes
3
replies
1.1k
views
Can't install Genesis
Genesis
Installation
updated 3.8 years ago by
Mike Smith
★ 6.0k • written 3.8 years ago by
winstondunnmd
▴ 10
0
votes
3
replies
757
views
GENESIS: ascertainment in GWAS
genesis
fitnullmodel
gwas
ascertainment
updated 3.8 years ago by
mconomos
▴ 70 • written 3.9 years ago by
ferranpauls10
• 0
6
votes
11
replies
2.0k
views
Genesis: doubts with admixMAPMM
genesis
admixmap
updated 4.1 years ago by
Stephanie M. Gogarten
▴ 840 • written 4.1 years ago by
GENOMIC_region
• 0
0
votes
1
reply
624
views
betas for binary outcome
genesis
4.2 years ago
Stephanie M. Gogarten
▴ 840
0
votes
13
replies
1.4k
views
GENESIS pcrelate() write gds file doesn't work
genesis
pcrelate
gds
updated 4.2 years ago by
Stephanie M. Gogarten
▴ 840 • written 4.2 years ago by
o.giannakopoulou
• 0
4
votes
2
replies
1.2k
views
Imputed dosages in GENESIS
genesis
gwastools
seqarray
4.6 years ago • updated 4.3 years ago
Stephanie M. Gogarten
▴ 840
0
votes
1
reply
649
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
4.3 years ago
naglemi
▴ 10
1
vote
1
reply
621
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS
GWAS
AssocTestMM
updated 4.5 years ago by
mconomos
▴ 70 • written 4.5 years ago by
naglemi
▴ 10
1
vote
1
reply
661
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis
pcrrelate
gds
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 840 • written 4.6 years ago by
roll
• 0
0
votes
1
reply
630
views
Using previously calculated PCs in GENESIS
genesis
snprelate
4.7 years ago
Stephanie M. Gogarten
▴ 840
0
votes
1
reply
682
views
Unable to build GDS with more than 255 scaffolds?
GENESIS
GWAS
GDS
updated 4.7 years ago by
zhengx
▴ 30 • written 4.7 years ago by
naglemi
▴ 10
0
votes
1
reply
520
views
selecting SNPs and samples in GENESIS
genesis
4.8 years ago
Stephanie M. Gogarten
▴ 840
0
votes
3
replies
844
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS
assoctestmm
GWAS
updated 4.9 years ago by
mconomos
▴ 70 • written 4.9 years ago by
naglemi
▴ 10
3
votes
4
replies
954
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM
GWAS
GENESIS
assocTestMM
updated 4.9 years ago by
mconomos
▴ 70 • written 4.9 years ago by
naglemi
▴ 10
2
votes
8
replies
1.2k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis
pcair
5.1 years ago
GENOMIC_region
• 0
0
votes
7
replies
1.2k
views
GENESIS: king2mat: subscript out of bounds
genesis
5.1 years ago
Stephanie M. Gogarten
▴ 840
33 results • Page
1 of 1
Recent ...
Replies
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Gordon Smyth
47k
Perhaps you are thinking of data analyses where the dependent variable is something other than expression itself. In the context of gene e…
Comment: Interpret plot from DiffBind
by
Chris
• 0
If I want to find genes that are more open in diseased than control, I can filter out peaks that have highest log2Fold change like this, is…
Comment: Interpret plot from DiffBind
by
Chris
• 0
Hi Rory. There are so many red dot above and below the blue line so it is hard to know which condition are more open, is that correct? Is 1…
Comment: Extract Limma Adjusted Values for Plotting
by
phelankj
• 0
Thanks, on the normalized values using the same formula?
Answer: Extract Limma Adjusted Values for Plotting
by
James W. MacDonald
63k
You should use `removeBatchEffect` for that.
Votes
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
Answer: Interpret plot from DiffBind
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