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DESeq2
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6
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19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 3 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
201
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
bioinf
▴ 10
2
votes
2
replies
88
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 6 hours ago by
Michael Love
41k • written 6 hours ago by
Reza
• 0
1
vote
4
replies
470
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 2 days ago
JKim
• 0
1
vote
1
reply
91
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
marcusn
• 0
0
votes
1
reply
114
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
angelathuynh5
• 0
0
votes
3
replies
229
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by
Michael Love
41k • written 3 days ago by
HAK
• 0
0
votes
3
replies
107
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
james.zhang20
• 0
0
votes
2
replies
70
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Espresso
• 0
0
votes
2
replies
102
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago
kcarey
• 0
0
votes
2
replies
103
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
3 days ago • updated 15 hours ago
Aurora
• 0
0
votes
5
replies
126
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 12 hours ago by
James W. MacDonald
65k • written 1 day ago by
arfranco
▴ 130
0
votes
0
replies
22
views
Handling multiple differential expression comparisons
DESeq2
7 hours ago
Zainab
• 0
0
votes
1
reply
91
views
putting my own expression data in deseq2
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
Dev
• 0
0
votes
1
reply
90
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
Agung
• 0
15 results • Page
1 of 1
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Replies
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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