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3
votes
9
replies
1.9k
views
Help with limma contrast, difference of a difference?
limma
23 months ago Ahdee ▴ 50
2
votes
1
reply
573
views
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
varian VariantToolsData
updated 23 months ago by 66k • written 24 months ago by ▴ 50
0
votes
3
replies
1.0k
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 2.2 years ago by 50k • written 2.3 years ago by ▴ 50
0
votes
0
replies
723
views
Is it possible to output ensembl id for annotatr build_annotations basicgenes?
Annotation annotatr
2.4 years ago Ahdee ▴ 50
0
votes
0
replies
865
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
2.4 years ago Ahdee ▴ 50
1
vote
2
replies
1.4k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
2.8 years ago Ahdee ▴ 50
1
vote
9
replies
2.0k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
3.0 years ago Ahdee ▴ 50
0
votes
3
replies
1.9k
views
How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 2.3 years ago by 50k • written 3.2 years ago by ▴ 50
2
votes
2
replies
769
views
In EdgeR TMM and/or voom is it better to normalize all samples, even if some will not be used for comparisons?
edger limma
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 50
1
vote
7
replies
2.1k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 3.2 years ago by • 0 • written 4.0 years ago by ▴ 50
0
votes
1
reply
715
views
Custom pathway for limma's kegga?
limma
4.1 years ago Ahdee ▴ 50
4
votes
7
replies
1.6k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 4.4 years ago by 50k • written 4.4 years ago by ▴ 50
0
votes
3
replies
1.2k
views
UnProducible error with goana and kegga function
limma goana kegga
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 50
2
votes
2
replies
955
views
How to create two columns for model matrix used in limma?
limma edger
updated 4.8 years ago by 50k • written 4.8 years ago by ▴ 50
4
votes
6
replies
690
views
Limma model design: is it better to just build a separate design for each specific comparison?
limma
updated 5.0 years ago by 66k • written 5.0 years ago by ▴ 50
1
vote
2
replies
1.1k
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 5.0 years ago by ▴ 160 • written 5.0 years ago by ▴ 50
0
votes
1
reply
820
views
Is there a package to convert DNA coordinates to Cytogenetic location?
annotation coordinates cytogenetic
5.1 years ago Ahdee ▴ 50
0
votes
0
replies
789
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
5.2 years ago Ahdee ▴ 50
4
votes
1
reply
2.5k
views
benefits of pearson distance for hierarchical clustering
heatmap.3 heatmap
updated 5.5 years ago by 66k • written 5.5 years ago by ▴ 50
4
votes
2
replies
2.0k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 50
3
votes
2
replies
866
views
Combining groups in a LIMMA design
limma
5.8 years ago Ahdee ▴ 50
2
votes
3
replies
731
views
Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
rnaseq limma edger
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 50
2
votes
2
replies
2.0k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 50
0
votes
1
reply
1.0k
views
Running model separately for each cell line or as the same model?
limma deseq2 edger rnaseq
updated 6.6 years ago by ▴ 120 • written 6.6 years ago by ▴ 50
2
votes
2
replies
1.2k
views
Why does total unique map not equal to library size?
htseqcounts star rnaseq
6.7 years ago Ahdee ▴ 50
0
votes
2
replies
917
views
LIMMA 2x2 with time
limma limma design matrix
updated 7.0 years ago by 66k • written 7.0 years ago by ▴ 50
0
votes
0
replies
1.2k
views
RPKM counts with SVA package & Combat with SVA?
batch effect combat sva sva
7.2 years ago Ahdee ▴ 50
1
vote
2
replies
1.0k
views
Treating 2 coefficients as the same group in Limma
limma glm
updated 7.6 years ago by 66k • written 7.6 years ago by ▴ 50
4
votes
10
replies
4.5k
views
Illumina MethylationEPIC vs. 450K
methylumi minfi illuminahumanmethylation450k.db 450k methyanalysis
updated 8.2 years ago by ▴ 740 • written 8.2 years ago by ▴ 50
1
vote
1
reply
5.0k
views
Combat generating negative values, should I log2 transform first?
combat batch effect
updated 8.6 years ago by ▴ 850 • written 8.6 years ago by ▴ 50
3
votes
2
replies
2.3k
views
How to use TopGO with gene symbols extracted from Illumina probes
topgo
updated 8.6 years ago by 66k • written 8.6 years ago by ▴ 50
6
votes
9
replies
1.6k
views
Help with 2x2 factorial for using LIMMA
limma design matrix limma
updated 8.6 years ago by 66k • written 8.6 years ago by ▴ 50
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