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genesis
•
reset
1
vote
2
replies
4.1k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 3.3 years ago by
Anna
• 0 • written 4.4 years ago by
solanum
• 0
6
votes
11
replies
2.8k
views
Genesis: doubts with admixMAPMM
genesis
admixmap
updated 5.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.0 years ago by
GENOMIC_region
• 0
0
votes
13
replies
2.3k
views
GENESIS pcrelate() write gds file doesn't work
genesis
pcrelate
gds
updated 5.2 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.2 years ago by
o.giannakopoulou
• 0
4
votes
2
replies
1.8k
views
Imputed dosages in GENESIS
genesis
gwastools
seqarray
5.6 years ago • updated 5.2 years ago
Stephanie M. Gogarten
▴ 870
0
votes
7
replies
1.8k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.0 years ago
Stephanie M. Gogarten
▴ 870
2
votes
8
replies
1.7k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis
pcair
6.0 years ago
GENOMIC_region
• 0
0
votes
3
replies
1.7k
views
Can't install Genesis
Genesis
Installation
updated 4.7 years ago by
Mike Smith
★ 6.5k • written 4.7 years ago by
winstondunnmd
▴ 10
0
votes
8
replies
1.5k
views
Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
4.2 years ago
alipka
▴ 10
3
votes
4
replies
1.5k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM
GWAS
GENESIS
assocTestMM
updated 5.8 years ago by
mconomos
▴ 70 • written 5.8 years ago by
naglemi
▴ 10
3
votes
6
replies
1.4k
views
Interpreting the output of score test using GENESIS
genesis
output
score
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
lassana.a.samarakoon
▴ 10
0
votes
3
replies
1.4k
views
Alternate allele for GENESIS?
genesis
effect allele
association analysis
updated 3.7 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.7 years ago by
ucbtapc
• 0
1
vote
3
replies
1.3k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
4.5 years ago
Corey.Cox
• 0
0
votes
3
replies
1.2k
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS
assoctestmm
GWAS
updated 5.8 years ago by
mconomos
▴ 70 • written 5.8 years ago by
naglemi
▴ 10
0
votes
3
replies
1.2k
views
GENESIS: ascertainment in GWAS
genesis
fitnullmodel
gwas
ascertainment
updated 4.8 years ago by
mconomos
▴ 70 • written 4.8 years ago by
ferranpauls10
• 0
0
votes
1
reply
1.1k
views
GENESIS multiple gds files
genesis
gds
SeqVarData
updated 3.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.9 years ago by
JT
• 0
2
votes
4
replies
1.1k
views
Sporadic missingness with admixmmap
genesis
admixmap
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
GENOMIC_region
• 0
1
vote
1
reply
1.0k
views
Calculating the z score from wald test association results in GENESIS
GENESIS
zscore
wald
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
lassana.a.samarakoon
▴ 10
0
votes
1
reply
981
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
5.3 years ago
naglemi
▴ 10
0
votes
1
reply
980
views
Unable to build GDS with more than 255 scaffolds?
GENESIS
GWAS
GDS
updated 5.6 years ago by
zhengx
▴ 30 • written 5.6 years ago by
naglemi
▴ 10
1
vote
1
reply
929
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS
GWAS
AssocTestMM
updated 5.5 years ago by
mconomos
▴ 70 • written 5.5 years ago by
naglemi
▴ 10
0
votes
1
reply
918
views
betas for binary outcome
genesis
5.1 years ago
Stephanie M. Gogarten
▴ 870
1
vote
1
reply
917
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis
pcrrelate
gds
updated 5.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.5 years ago by
roll
• 0
0
votes
1
reply
909
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.6 years ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
908
views
Association testing model in GENESIS
genesis
updated 3.8 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.8 years ago by
o.giannakopoulou
• 0
0
votes
0
replies
865
views
Normalisation of Data before loading in TMixClust
rna-seq
tmixclust
k-means clustering
gene expression
genesis
4.4 years ago
astridite
• 0
0
votes
1
reply
850
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago
Stephanie M. Gogarten
▴ 870
2
votes
1
reply
809
views
Why did the Wald test disappear from GENESIS?
genesis
4.5 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
789
views
using GENESIS R package with non-human species
genesis
gwastools
3.8 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
785
views
selecting SNPs and samples in GENESIS
genesis
5.7 years ago
Stephanie M. Gogarten
▴ 870
2
votes
5
replies
776
views
assocTestSingle output with GxE
GENESIS
updated 10 months ago by
Stephanie M. Gogarten
▴ 870 • written 10 months ago by
SuperDad
• 0
0
votes
2
replies
710
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix
GENESIS
Plants
18 months ago
Monica
• 0
0
votes
0
replies
686
views
X chromosome analyses for males in GENESIS
GENESIS
3.5 years ago
Stephanie M. Gogarten
▴ 870
2
votes
1
reply
673
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.3 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.3 years ago by
lassana.a.samarakoon
▴ 10
1
vote
1
reply
452
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS
autosome-only=FALSE?
PCAir
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
gabry.scata
• 0
0
votes
1
reply
444
views
Reference categories for factors
assocTestSingle
GENESIS
written 15 months ago by
SuperD
• 0
0
votes
2
replies
420
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 5 months ago by
Stephanie M. Gogarten
▴ 870 • written 5 months ago by
Mindy wang
• 0
0
votes
2
replies
400
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS
SeqVarTools
updated 6 months ago by
Stephanie M. Gogarten
▴ 870 • written 6 months ago by
pjuge
• 0
0
votes
0
replies
278
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS
admixMap
6 months ago
mailtoshivam13
• 0
0
votes
1
reply
215
views
GENESIS: error in crossprod
GENESIS
11 weeks ago
Stephanie M. Gogarten
▴ 870
39 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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