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seqArray
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SeqArray_1.19.2, SeqArray::info() for example gds data does not return correct character list for `AA` column
SeqArray
info
SeqArray::info()
6.3 years ago
qliu7
• 0
1
vote
3
replies
1.2k
views
seqVCF2GDS Error Converting VCF to GDS file
software error
SeqArray
seqVCF2GDS
updated 4.7 years ago by
zhengx
▴ 30 • written 4.7 years ago by
winstondunnmd
▴ 10
0
votes
2
replies
935
views
SeqArray problem in seqVCF2GDS and convert back to vcf
SeqArray
updated 5.1 years ago by
zhengx
▴ 30 • written 5.2 years ago by
miyouduniu
• 0
0
votes
2
replies
1.3k
views
Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems with vcf.fn
seqarray
updated 5.7 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.7 years ago by
cav3gh
• 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
1
vote
1
reply
1.4k
views
How to imports DS field from VCF files with SeqArray seqVCF2GDS()
seqArray
seqVCF2GDS
updated 3.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.9 years ago by
ealopera
• 0
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Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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