Showing : genesis • reset
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231
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Conditional analysis
GENESIS
6 months ago SuperDad • 0
0
votes
1
reply
442
views
GENESIS: error in crossprod
GENESIS
9 months ago Stephanie M. Gogarten ▴ 870
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2
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722
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 11 months ago by ▴ 870 • written 11 months ago by • 0
0
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2
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631
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 12 months ago by ▴ 870 • written 12 months ago by • 0
1
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1
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767
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 12 months ago by 67k • written 12 months ago by ▴ 10
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484
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
13 months ago mailtoshivam13 • 0
2
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5
replies
1.0k
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assocTestSingle output with GxE
GENESIS
updated 17 months ago by ▴ 870 • written 17 months ago by • 0
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1
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572
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Reference categories for factors
assocTestSingle GENESIS
written 21 months ago by • 0
0
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2
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911
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
2.1 years ago Monica • 0
1
vote
2
replies
4.7k
views
Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 3.8 years ago by • 0 • written 5.0 years ago by • 0
0
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1
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1.0k
views
Approximations to Est and Est.SE in GENESIS
GENESIS
4.0 years ago Stephanie M. Gogarten ▴ 870
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0
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819
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X chromosome analyses for males in GENESIS
GENESIS
4.0 years ago Stephanie M. Gogarten ▴ 870
0
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3
replies
1.7k
views
Alternate allele for GENESIS?
genesis effect allele association analysis
updated 4.3 years ago by ▴ 870 • written 4.3 years ago by • 0
0
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1
reply
947
views
using GENESIS R package with non-human species
genesis gwastools
4.3 years ago Stephanie M. Gogarten ▴ 870
0
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2
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1.1k
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Association testing model in GENESIS
genesis
updated 4.4 years ago by ▴ 870 • written 4.4 years ago by • 0
0
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1
reply
1.4k
views
GENESIS multiple gds files
genesis gds SeqVarData
updated 4.4 years ago by ▴ 870 • written 4.5 years ago by • 0
0
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8
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1.8k
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Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
4.8 years ago alipka ▴ 10
2
votes
1
reply
820
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.8 years ago by ▴ 870 • written 4.8 years ago by ▴ 10
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0
replies
1.0k
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.0 years ago astridite • 0
2
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1
reply
965
views
Why did the Wald test disappear from GENESIS?
genesis
5.0 years ago Stephanie M. Gogarten ▴ 870
1
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3
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1.5k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
5.1 years ago Corey.Cox • 0
1
vote
1
reply
1.2k
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by ▴ 10
3
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6
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1.7k
views
Interpreting the output of score test using GENESIS
genesis output score
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by ▴ 10
2
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4
replies
1.3k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 5.2 years ago by ▴ 870 • written 5.2 years ago by • 0
0
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3
replies
2.0k
views
Can't install Genesis
Genesis Installation
updated 5.3 years ago by ★ 6.6k • written 5.3 years ago by ▴ 10
0
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3
replies
1.4k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 5.3 years ago by ▴ 70 • written 5.3 years ago by • 0
6
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11
replies
3.1k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 5.6 years ago by ▴ 870 • written 5.6 years ago by • 0
0
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1
reply
1.1k
views
betas for binary outcome
genesis
5.7 years ago Stephanie M. Gogarten ▴ 870
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13
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2.7k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 5.7 years ago by ▴ 870 • written 5.7 years ago by • 0
4
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2
replies
2.0k
views
Imputed dosages in GENESIS
genesis gwastools seqarray
6.1 years ago • updated 5.8 years ago Stephanie M. Gogarten ▴ 870
0
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1
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1.1k
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.8 years ago naglemi ▴ 10
1
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1
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1.1k
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 6.0 years ago by ▴ 70 • written 6.0 years ago by ▴ 10
1
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1
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1.1k
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 6.1 years ago by ▴ 870 • written 6.1 years ago by • 0
0
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1
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1.0k
views
Using previously calculated PCs in GENESIS
genesis snprelate
6.2 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
1.2k
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 6.2 years ago by ▴ 30 • written 6.2 years ago by ▴ 10
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1
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900
views
selecting SNPs and samples in GENESIS
genesis
6.3 years ago Stephanie M. Gogarten ▴ 870
0
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3
replies
1.4k
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 10
3
votes
4
replies
1.7k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 10
2
votes
8
replies
1.9k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis pcair
6.5 years ago GENOMIC_region • 0
0
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7
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2.1k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.5 years ago Stephanie M. Gogarten ▴ 870
40 results • Page 1 of 1
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Replies
Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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