Showing : GENESIS • reset
6
votes
11
replies
2.8k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 5.0 years ago by ▴ 870 • written 5.0 years ago by • 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
3
votes
6
replies
1.4k
views
Interpreting the output of score test using GENESIS
genesis output score
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 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 ▴ 70 • written 5.8 years ago by ▴ 10
2
votes
1
reply
671
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.3 years ago by ▴ 870 • written 4.3 years ago by ▴ 10
2
votes
4
replies
1.1k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by • 0
2
votes
5
replies
776
views
assocTestSingle output with GxE
GENESIS
updated 10 months ago by ▴ 870 • written 10 months ago by • 0
2
votes
1
reply
809
views
Why did the Wald test disappear from GENESIS?
genesis
4.5 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
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 • 0 • written 4.4 years ago by • 0
1
vote
1
reply
914
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 5.5 years ago by ▴ 870 • written 5.5 years ago by • 0
1
vote
1
reply
449
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 5 months ago by 65k • written 5 months ago by • 0
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 ▴ 70 • written 5.5 years ago by ▴ 10
1
vote
1
reply
1000
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
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
1.4k
views
Alternate allele for GENESIS?
genesis effect allele association analysis
updated 3.7 years ago by ▴ 870 • written 3.7 years ago by • 0
0
votes
0
replies
686
views
X chromosome analyses for males in GENESIS
GENESIS
3.5 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
845
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
0
votes
2
replies
400
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 5 months ago by ▴ 870 • written 5 months ago by • 0
0
votes
2
replies
708
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 0
0
votes
1
reply
442
views
Reference categories for factors
assocTestSingle GENESIS
written 14 months ago by • 0
0
votes
2
replies
416
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 5 months ago by ▴ 870 • written 5 months ago by • 0
0
votes
0
replies
277
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
6 months ago mailtoshivam13 • 0
0
votes
7
replies
1.8k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.0 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
213
views
GENESIS: error in crossprod
GENESIS
11 weeks 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 5.8 years ago by ▴ 70 • written 5.8 years ago by ▴ 10
0
votes
1
reply
784
views
selecting SNPs and samples in GENESIS
genesis
5.7 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
979
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 5.6 years ago by ▴ 30 • written 5.6 years ago by ▴ 10
0
votes
1
reply
907
views
Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
977
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.2 years ago naglemi ▴ 10
0
votes
13
replies
2.3k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 5.2 years ago by ▴ 870 • written 5.2 years ago by • 0
0
votes
1
reply
914
views
betas for binary outcome
genesis
5.1 years ago Stephanie M. Gogarten ▴ 870
0
votes
3
replies
1.2k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by • 0
0
votes
3
replies
1.7k
views
Can't install Genesis
Genesis Installation
updated 4.7 years ago by ★ 6.5k • written 4.7 years ago by ▴ 10
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
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
0
votes
1
reply
1.1k
views
GENESIS multiple gds files
genesis gds SeqVarData
updated 3.9 years ago by ▴ 870 • written 3.9 years ago by • 0
0
votes
2
replies
907
views
Association testing model in GENESIS
genesis
updated 3.8 years ago by ▴ 870 • written 3.8 years ago by • 0
0
votes
1
reply
789
views
using GENESIS R package with non-human species
genesis gwastools
3.8 years ago Stephanie M. Gogarten ▴ 870
39 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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