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 5.3 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
673
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 4.7 years ago by ▴ 870 • written 4.7 years ago by • 0
2
votes
5
replies
780
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
921
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
458
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 6 months ago by 65k • written 6 months ago by • 0
1
vote
1
reply
931
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
1.0k
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
4.6 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
691
views
X chromosome analyses for males in GENESIS
GENESIS
3.5 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
852
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
0
votes
2
replies
410
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 6 months ago by ▴ 870 • written 6 months ago by • 0
0
votes
2
replies
712
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 0
0
votes
1
reply
447
views
Reference categories for factors
assocTestSingle GENESIS
written 15 months ago by • 0
0
votes
2
replies
423
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
285
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
222
views
GENESIS: error in crossprod
GENESIS
12 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
788
views
selecting SNPs and samples in GENESIS
genesis
5.8 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
983
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
910
views
Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
983
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.3 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
918
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
866
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
912
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
791
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
Recent ...
Replies
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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