Showing : genesis • reset
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207
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GENESIS: error in crossprod
GENESIS
10 weeks ago Stephanie M. Gogarten ▴ 870
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2
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407
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 4 months ago by ▴ 870 • written 4 months ago by • 0
0
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2
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392
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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
1
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1
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444
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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
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0
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272
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
6 months ago mailtoshivam13 • 0
2
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5
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771
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assocTestSingle output with GxE
GENESIS
updated 10 months ago by ▴ 870 • written 10 months ago by • 0
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1
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437
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Reference categories for factors
assocTestSingle GENESIS
written 14 months ago by • 0
0
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2
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706
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 0
1
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2
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4.1k
views
Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 3.2 years ago by • 0 • written 4.4 years ago by • 0
0
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1
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834
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Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
0
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0
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682
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X chromosome analyses for males in GENESIS
GENESIS
3.5 years ago Stephanie M. Gogarten ▴ 870
0
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3
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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
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1
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787
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using GENESIS R package with non-human species
genesis gwastools
3.8 years ago Stephanie M. Gogarten ▴ 870
0
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2
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902
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Association testing model in GENESIS
genesis
updated 3.8 years ago by ▴ 870 • written 3.8 years ago by • 0
0
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1
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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
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8
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1.5k
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Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
4.2 years ago alipka ▴ 10
2
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1
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665
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.2 years ago by ▴ 870 • written 4.3 years ago by ▴ 10
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0
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863
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
4.4 years ago astridite • 0
2
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1
reply
808
views
Why did the Wald test disappear from GENESIS?
genesis
4.5 years ago Stephanie M. Gogarten ▴ 870
1
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3
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1.3k
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Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
4.5 years ago Corey.Cox • 0
1
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1
reply
997
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
3
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6
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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
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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
0
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3
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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
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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
6
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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
0
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1
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913
views
betas for binary outcome
genesis
5.1 years ago Stephanie M. Gogarten ▴ 870
0
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13
replies
2.3k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 5.1 years ago by ▴ 870 • written 5.2 years ago by • 0
4
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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
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1
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973
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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
1
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1
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927
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 5.4 years ago by ▴ 70 • written 5.4 years ago by ▴ 10
1
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1
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909
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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
0
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1
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903
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Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
0
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1
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977
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
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1
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781
views
selecting SNPs and samples in GENESIS
genesis
5.7 years ago Stephanie M. Gogarten ▴ 870
0
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3
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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
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
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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
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7
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1.8k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.0 years ago Stephanie M. Gogarten ▴ 870
39 results • Page 1 of 1
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Replies
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Awards • All
Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
Centurion to Chris • 0
Commentator to Leonard Goldstein ▴ 200
Popular Question to Matthew Ritchie ▴ 1000
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