Showing : GENESIS • reset
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190
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GENESIS: error in crossprod
GENESIS
9 weeks ago Stephanie M. Gogarten ▴ 870
0
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2
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378
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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
votes
2
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383
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
1
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1
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429
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
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0
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261
views
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
replies
753
views
assocTestSingle output with GxE
GENESIS
updated 9 months ago by ▴ 870 • written 10 months ago by • 0
0
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1
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424
views
Reference categories for factors
assocTestSingle GENESIS
written 14 months ago by • 0
0
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2
replies
692
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 0
1
vote
2
replies
4.0k
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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822
views
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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670
views
X chromosome analyses for males in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
0
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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
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1
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777
views
using GENESIS R package with non-human species
genesis gwastools
3.7 years ago Stephanie M. Gogarten ▴ 870
0
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2
replies
890
views
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 3.8 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
votes
1
reply
652
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.2 years ago by ▴ 870 • written 4.2 years ago by ▴ 10
0
votes
0
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849
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
4.4 years ago astridite • 0
2
votes
1
reply
793
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
4.5 years ago Corey.Cox • 0
1
vote
1
reply
976
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 4.5 years ago by ▴ 870 • written 4.5 years ago by ▴ 10
3
votes
6
replies
1.4k
views
Interpreting the output of score test using GENESIS
genesis output score
updated 4.5 years ago by ▴ 870 • written 4.5 years ago by ▴ 10
2
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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
replies
1.6k
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
1.1k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 4.7 years ago by ▴ 70 • written 4.7 years ago by • 0
6
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11
replies
2.7k
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
reply
905
views
betas for binary outcome
genesis
5.0 years ago Stephanie M. Gogarten ▴ 870
0
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13
replies
2.2k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by • 0
4
votes
2
replies
1.8k
views
Imputed dosages in GENESIS
genesis gwastools seqarray
5.5 years ago • updated 5.2 years ago Stephanie M. Gogarten ▴ 870
0
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1
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960
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
1
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1
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913
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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893
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
0
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1
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894
views
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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961
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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770
views
selecting SNPs and samples in GENESIS
genesis
5.7 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 ▴ 70 • written 5.7 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 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 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
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7
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1.8k
views
GENESIS: king2mat: subscript out of bounds
genesis
5.9 years ago Stephanie M. Gogarten ▴ 870
39 results • Page 1 of 1
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Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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