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4
votes
9
replies
2.2k
views
tximport recommendation for limma-trend downstream analysis?
tximport limma limma-trend edgeR
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ★ 2.0k
0
votes
0
replies
1.4k
views
Comment: C: prior.prob has opposite effects in goana and kegga?
6.8 years ago Jenny Drnevich ★ 2.0k
0
votes
2
replies
1.4k
views
prior.prob has opposite effects in goana and kegga?
limma missMethyl gometh goana kegga
updated 6.8 years ago by 50k • written 6.9 years ago by ★ 2.0k
0
votes
1
reply
723
views
bug in kegga() when using prior.prob?
limma edgeR
updated 6.8 years ago by 50k • written 6.8 years ago by ★ 2.0k
1
vote
0
replies
929
views
Answer: A: Plotting Gene Expression Data From Multiple Batches
6.8 years ago Jenny Drnevich ★ 2.0k
0
votes
11
replies
3.7k
views
bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype arguments
DMRcate minfi
updated 12 weeks ago by ▴ 170 • written 7.1 years ago by ★ 2.0k
0
votes
1
reply
1.9k
views
Comment: C: raw probe set expression data and masking questions
7.1 years ago Jenny Drnevich ★ 2.0k
1
vote
0
replies
1.7k
views
Comment: C: goseq Error: could not find function "supportedOrganisms"
7.1 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
1.9k
views
Comment: C: raw probe set expression data and masking questions
7.1 years ago Jenny Drnevich ★ 2.0k
1
vote
2
replies
2.4k
views
read.metharray() not recognizing some of my EPIC arrays; force = TRUE not working either
minfi
7.1 years ago Jenny Drnevich ★ 2.0k
5
votes
1
reply
13k
views
Answer: C: Limma: how to get same output as topTable but for all the genes ?
updated 7.2 years ago by 50k • written 15.4 years ago by ★ 2.0k
0
votes
1
reply
4.8k
views
Comment: C: Easy way to turn OrgDb object from AnnotationHub into package?
7.2 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
4.8k
views
Comment: C: Easy way to turn OrgDb object from AnnotationHub into package?
7.2 years ago Jenny Drnevich ★ 2.0k
0
votes
14
replies
4.8k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub AnnotationDbi AnnotationForge pathview
7.2 years ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.2k
views
Comment: C: How to define contrasts for expression changes over time
7.2 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.3k
views
Comment: C: Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization
7.2 years ago Jenny Drnevich ★ 2.0k
0
votes
3
replies
1.3k
views
Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization not available..."
affycoretools
updated 7.2 years ago by 65k • written 7.2 years ago by ★ 2.0k
0
votes
0
replies
1.3k
views
Answer: A: Problem after upgrading from affycoretools 1.46.1 to 1.46.3; "vfs customization
7.2 years ago Jenny Drnevich ★ 2.0k
3
votes
2
replies
6.6k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 7.5 years ago by 41k • written 7.5 years ago by ★ 2.0k
0
votes
0
replies
13k
views
Answer: A: Problem with installation of org.Hs.eg.db
7.5 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.4k
views
Comment: C: How to remove nested batch effects with removeBatchEffect?
7.5 years ago Jenny Drnevich ★ 2.0k
0
votes
3
replies
1.4k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ★ 2.0k
0
votes
0
replies
4.2k
views
Comment: C: voom + removeBatchEffect + gene clustering
7.5 years ago Jenny Drnevich ★ 2.0k
1
vote
1
reply
4.2k
views
Comment: C: voom + removeBatchEffect + gene clustering
7.6 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
2.9k
views
Comment: C: Problem with tximport(reader = read_tsv) and workaround
7.6 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
2.9k
views
Comment: C: Problem with tximport(reader = read_tsv) and workaround
7.6 years ago Jenny Drnevich ★ 2.0k
5
votes
5
replies
2.9k
views
Problem with tximport(reader = read_tsv) and workaround
tximport readr read_tsv
updated 7.6 years ago by 41k • written 7.6 years ago by ★ 2.0k
2
votes
3
replies
1.4k
views
Problems with running limma voom on subsets of genes from WGCNA modules?
WGCNA limma voom
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ★ 2.0k
0
votes
0
replies
1.4k
views
Comment: C: Problems with running limma voom on subsets of genes from WGCNA modules?
7.6 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
2.5k
views
Comment: C: Find if a covariate has effect on gene expression level using edgeR and DESeq2
7.6 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
1.4k
views
Comment: C: AnnotationHub's NCBI OrgDB have older EGSOURCEDATE than org.Xy.eg.db?
7.6 years ago Jenny Drnevich ★ 2.0k
0
votes
3
replies
1.4k
views
AnnotationHub's NCBI OrgDB have older EGSOURCEDATE than org.Xy.eg.db?
AnnotationHub
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by ★ 2.0k
1
vote
1
reply
2.5k
views
Answer: A: Find if a covariate has effect on gene expression level using edgeR and DESeq2
7.6 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.7k
views
Differential protein abundance testing using emPAI values?
proteomics limma
7.7 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.0k
views
Comment: C: bug in Glimma - anno can't have T/F
7.8 years ago Jenny Drnevich ★ 2.0k
1
vote
2
replies
1.0k
views
bug in Glimma - anno can't have T/F
Glimma
7.8 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
973
views
Comment: C: Missing binaries for AnnotationData packages?
updated 8.1 years ago by 65k • written 8.1 years ago by ★ 2.0k
0
votes
5
replies
973
views
Missing binaries for AnnotationData packages?
binary
8.1 years ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
973
views
Answer: A: Missing binaries for AnnotationData packages?
8.1 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
973
views
Comment: C: Missing binaries for AnnotationData packages?
updated 8.1 years ago by ★ 8.2k • written 8.1 years ago by ★ 2.0k
0
votes
0
replies
1.3k
views
Answer: A: Collation of differentially expressed genes in Limma
8.3 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
6.1k
views
Comment: C: sva + egdeR - differential expression analysis - RNA-seq data
8.3 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
11k
views
Comment: C: trouble using select() to get all GO terms when have duplicate query IDs
updated 8.4 years ago by 25k • written 8.4 years ago by ★ 2.0k
0
votes
3
replies
11k
views
trouble using select() to get all GO terms when have duplicate query IDs
AnnotationDbi
updated 8.4 years ago by 65k • written 8.4 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
Comment: C: rtracklayer v1.30.0 can no longer import gff files
8.5 years ago Jenny Drnevich ★ 2.0k
0
votes
3
replies
1.3k
views
rtracklayer v1.30.0 can no longer import gff files
rtracklayer import.gff3 bug
updated 8.5 years ago by 16k • written 8.5 years ago by ★ 2.0k
0
votes
0
replies
2.2k
views
Comment: C: design matrix for cross-over + repeated measures in limma?
8.6 years ago Jenny Drnevich ★ 2.0k
3
votes
5
replies
2.2k
views
design matrix for cross-over + repeated measures in limma?
limma
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ★ 2.0k
1
vote
0
replies
6.0k
views
Comment: C: edgeR Normalization Method
8.7 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.7k
views
Comment: C: SCAN-normalized values on log2 scale?
updated 8.7 years ago by 65k • written 8.7 years ago by ★ 2.0k
288 results • Page 2 of 6
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