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Comment: Comment: Help with limma contrast, difference of a difference?
22 months ago Ahdee ▴ 50
0
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0
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1.9k
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Comment: Comment: Help with limma contrast, difference of a difference?
22 months ago Ahdee ▴ 50
0
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1
reply
1.9k
views
Comment: Comment: Help with limma contrast, difference of a difference?
22 months ago Ahdee ▴ 50
3
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9
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1.9k
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Help with limma contrast, difference of a difference?
limma
22 months ago Ahdee ▴ 50
0
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1
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1.9k
views
Comment: Comment: Help with limma contrast, difference of a difference?
22 months ago Ahdee ▴ 50
2
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1
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551
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Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
varian VariantToolsData
updated 22 months ago by 65k • written 23 months ago by ▴ 50
0
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1
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990
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Comment: Comment: Need help with a contrast design for limma with a missing group?
2.2 years ago Ahdee ▴ 50
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3
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990
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Need help with a contrast design for limma with a missing group?
limma VOOM
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 50
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0
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696
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Is it possible to output ensembl id for annotatr build_annotations basicgenes?
Annotation annotatr
2.4 years ago Ahdee ▴ 50
0
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0
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824
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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
0
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0
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1.4k
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Comment: Comment: Confused about using ComBat_seq with voom and limma? Should run batch as a cova
2.7 years ago Ahdee ▴ 50
0
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0
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3.2k
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Comment: Comment: How to count barcode sequences in a fastq file
2.7 years ago Ahdee ▴ 50
1
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2
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1.4k
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Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
2.7 years ago Ahdee ▴ 50
0
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0
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1.9k
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Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
2.9 years ago Ahdee ▴ 50
0
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1
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1.9k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
2.9 years ago Ahdee ▴ 50
0
votes
1
reply
1.9k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
2.9 years ago Ahdee ▴ 50
1
vote
9
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1.9k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
2.9 years ago Ahdee ▴ 50
0
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0
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1.9k
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Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
2.9 years ago Ahdee ▴ 50
0
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1
reply
1.8k
views
Comment: Comment: How to calculate coefficient of variation within group?
3.1 years ago Ahdee ▴ 50
0
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3
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1.8k
views
How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 2.2 years ago by 50k • written 3.1 years ago by ▴ 50
0
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0
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752
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Comment: C: In EdgeR TMM and/or voom is it better to normalize all samples, even if some wil
3.7 years ago Ahdee ▴ 50
2
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2
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752
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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 3.7 years ago by 50k • written 3.7 years ago by ▴ 50
0
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1
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2.1k
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Comment: C: tximport from RSEM expected counts: is it possible to import from a table rather
3.7 years ago Ahdee ▴ 50
1
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7
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2.1k
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tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 3.1 years ago by • 0 • written 3.9 years ago by ▴ 50
0
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0
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692
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Answer: A: Custom pathway for limma's kegga?
4.0 years ago Ahdee ▴ 50
0
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1
reply
692
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Custom pathway for limma's kegga?
limma
4.0 years ago Ahdee ▴ 50
0
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0
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1.5k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.4 years ago Ahdee ▴ 50
0
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0
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1.5k
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Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.4 years ago Ahdee ▴ 50
0
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1
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1.5k
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Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.4 years ago Ahdee ▴ 50
0
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1
reply
1.5k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.4 years ago Ahdee ▴ 50
4
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7
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1.5k
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
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1
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1.2k
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Comment: C: UnProducible error with goana and kegga function
4.6 years ago Ahdee ▴ 50
0
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3
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1.2k
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UnProducible error with goana and kegga function
limma goana kegga
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 50
0
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0
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909
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Comment: C: How to create two columns for model matrix used in limma?
4.6 years ago Ahdee ▴ 50
2
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2
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909
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How to create two columns for model matrix used in limma?
limma edger
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 50
0
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1
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668
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Comment: C: Limma model design: is it better to just build a separate design for each specif
4.9 years ago Ahdee ▴ 50
0
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1
reply
668
views
Comment: C: Limma model design: is it better to just build a separate design for each specif
4.9 years ago Ahdee ▴ 50
4
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6
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668
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Limma model design: is it better to just build a separate design for each specific comparison?
limma
updated 4.9 years ago by 65k • written 4.9 years ago by ▴ 50
0
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0
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1.0k
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Comment: C: Why does limma voom E value give different result than the voom object
4.9 years ago Ahdee ▴ 50
0
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0
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11k
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Comment: C: Seurat 2.3.4 installation
4.9 years ago Ahdee ▴ 50
1
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2
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1.0k
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 4.9 years ago by ▴ 160 • written 4.9 years ago by ▴ 50
0
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1
reply
797
views
Is there a package to convert DNA coordinates to Cytogenetic location?
annotation coordinates cytogenetic
5.1 years ago Ahdee ▴ 50
0
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0
replies
772
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
5.1 years ago Ahdee ▴ 50
4
votes
1
reply
2.4k
views
benefits of pearson distance for hierarchical clustering
heatmap.3 heatmap
updated 5.4 years ago by 65k • written 5.4 years ago by ▴ 50
0
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0
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2.0k
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Comment: C: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
5.7 years ago Ahdee ▴ 50
4
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2
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2.0k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 50
0
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0
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853
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Comment: C: Combining groups in a LIMMA design
5.7 years ago Ahdee ▴ 50
3
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2
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853
views
Combining groups in a LIMMA design
limma
5.7 years ago Ahdee ▴ 50
0
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0
replies
715
views
Comment: C: Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
5.8 years ago Ahdee ▴ 50
2
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3
replies
715
views
Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
rnaseq limma edger
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 50
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