Showing : rna-seq • reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 15 days ago by • 0 • written 8.8 years ago by ▴ 30
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
4
replies
867
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
3
votes
3
replies
326
views
permutation test in edgeR
rna-seq edgeR
updated 12 days ago by 50k • written 25 days ago by • 0
2
votes
2
replies
89
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 hours ago by 41k • written 8 hours ago by • 0
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
votes
1
reply
908
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 4 months ago by ★ 4.1k • written 6.0 years ago by • 0
0
votes
10
replies
2.2k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 5.1 years ago by • 0
0
votes
3
replies
712
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 11 months ago by 65k • written 11 months ago by • 0
0
votes
3
replies
655
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
votes
3
replies
851
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 11 months ago by 65k • written 11 months ago by • 0
0
votes
2
replies
312
views
WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
0
votes
3
replies
683
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 41k • written 10 months ago by • 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 0
0
votes
4
replies
706
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago • updated 6 months ago ar14g12 • 0
17 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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