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genesis
•
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0
votes
1
reply
158
views
GENESIS: error in crossprod
GENESIS
6 weeks ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
337
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 3 months ago by
Stephanie M. Gogarten
▴ 870 • written 3 months ago by
Mindy wang
• 0
0
votes
2
replies
355
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS
SeqVarTools
updated 4 months ago by
Stephanie M. Gogarten
▴ 870 • written 4 months ago by
pjuge
• 0
1
vote
1
reply
400
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS
autosome-only=FALSE?
PCAir
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
gabry.scata
• 0
0
votes
0
replies
243
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS
admixMap
5 months ago
mailtoshivam13
• 0
2
votes
5
replies
720
views
assocTestSingle output with GxE
GENESIS
updated 9 months ago by
Stephanie M. Gogarten
▴ 870 • written 9 months ago by
SuperDad
• 0
0
votes
1
reply
395
views
Reference categories for factors
assocTestSingle
GENESIS
written 13 months ago by
SuperD
• 0
0
votes
2
replies
668
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix
GENESIS
Plants
17 months ago
Monica
• 0
1
vote
2
replies
3.9k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 3.2 years ago by
Anna
• 0 • written 4.3 years ago by
solanum
• 0
0
votes
1
reply
798
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.3 years ago
Stephanie M. Gogarten
▴ 870
0
votes
0
replies
646
views
X chromosome analyses for males in GENESIS
GENESIS
3.4 years ago
Stephanie M. Gogarten
▴ 870
0
votes
3
replies
1.3k
views
Alternate allele for GENESIS?
genesis
effect allele
association analysis
updated 3.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.6 years ago by
ucbtapc
• 0
0
votes
1
reply
761
views
using GENESIS R package with non-human species
genesis
gwastools
3.7 years ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
867
views
Association testing model in GENESIS
genesis
updated 3.7 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.7 years ago by
o.giannakopoulou
• 0
0
votes
1
reply
1.1k
views
GENESIS multiple gds files
genesis
gds
SeqVarData
updated 3.8 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.8 years ago by
JT
• 0
0
votes
8
replies
1.5k
views
Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
4.1 years ago
alipka
▴ 10
2
votes
1
reply
632
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.2 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.2 years ago by
lassana.a.samarakoon
▴ 10
0
votes
0
replies
829
views
Normalisation of Data before loading in TMixClust
rna-seq
tmixclust
k-means clustering
gene expression
genesis
4.3 years ago
astridite
• 0
2
votes
1
reply
780
views
Why did the Wald test disappear from GENESIS?
genesis
4.4 years ago
Stephanie M. Gogarten
▴ 870
1
vote
3
replies
1.3k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
4.4 years ago
Corey.Cox
• 0
1
vote
1
reply
959
views
Calculating the z score from wald test association results in GENESIS
GENESIS
zscore
wald
updated 4.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.5 years ago by
lassana.a.samarakoon
▴ 10
3
votes
6
replies
1.3k
views
Interpreting the output of score test using GENESIS
genesis
output
score
updated 4.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.5 years ago by
lassana.a.samarakoon
▴ 10
2
votes
4
replies
1.0k
views
Sporadic missingness with admixmmap
genesis
admixmap
updated 4.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.5 years ago by
GENOMIC_region
• 0
0
votes
3
replies
1.6k
views
Can't install Genesis
Genesis
Installation
updated 4.6 years ago by
Mike Smith
★ 6.5k • written 4.6 years ago by
winstondunnmd
▴ 10
0
votes
3
replies
1.1k
views
GENESIS: ascertainment in GWAS
genesis
fitnullmodel
gwas
ascertainment
updated 4.7 years ago by
mconomos
▴ 70 • written 4.7 years ago by
ferranpauls10
• 0
6
votes
11
replies
2.7k
views
Genesis: doubts with admixMAPMM
genesis
admixmap
updated 4.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.9 years ago by
GENOMIC_region
• 0
0
votes
1
reply
872
views
betas for binary outcome
genesis
5.0 years ago
Stephanie M. Gogarten
▴ 870
0
votes
13
replies
2.2k
views
GENESIS pcrelate() write gds file doesn't work
genesis
pcrelate
gds
updated 5.1 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
o.giannakopoulou
• 0
4
votes
2
replies
1.7k
views
Imputed dosages in GENESIS
genesis
gwastools
seqarray
5.5 years ago • updated 5.1 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
927
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
5.1 years ago
naglemi
▴ 10
1
vote
1
reply
902
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS
GWAS
AssocTestMM
updated 5.4 years ago by
mconomos
▴ 70 • written 5.4 years ago by
naglemi
▴ 10
1
vote
1
reply
873
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis
pcrrelate
gds
updated 5.4 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.4 years ago by
roll
• 0
0
votes
1
reply
871
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.5 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
939
views
Unable to build GDS with more than 255 scaffolds?
GENESIS
GWAS
GDS
updated 5.5 years ago by
zhengx
▴ 30 • written 5.5 years ago by
naglemi
▴ 10
0
votes
1
reply
752
views
selecting SNPs and samples in GENESIS
genesis
5.6 years ago
Stephanie M. Gogarten
▴ 870
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 5.7 years ago by
mconomos
▴ 70 • written 5.7 years ago by
naglemi
▴ 10
3
votes
4
replies
1.4k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM
GWAS
GENESIS
assocTestMM
updated 5.7 years ago by
mconomos
▴ 70 • written 5.7 years ago by
naglemi
▴ 10
2
votes
8
replies
1.6k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis
pcair
5.9 years ago
GENOMIC_region
• 0
0
votes
7
replies
1.7k
views
GENESIS: king2mat: subscript out of bounds
genesis
5.9 years ago
Stephanie M. Gogarten
▴ 870
39 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
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