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DESeq2
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6
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172
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Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 2 days ago by
arfranco
▴ 130
2
votes
2
replies
117
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Reza
• 0
0
votes
0
replies
41
views
Handling multiple differential expression comparisons
DESeq2
1 day ago
Zainab
• 0
0
votes
2
replies
82
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Espresso
• 0
0
votes
2
replies
117
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
3 days ago • updated 2 days ago
kcarey
• 0
0
votes
3
replies
117
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
james.zhang20
• 0
0
votes
1
reply
125
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
angelathuynh5
• 0
0
votes
3
replies
237
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
HAK
• 0
1
vote
1
reply
99
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
marcusn
• 0
0
votes
2
replies
113
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 1 day ago
Aurora
• 0
0
votes
1
reply
97
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
Agung
• 0
0
votes
1
reply
98
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Dev
• 0
3
votes
3
replies
218
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
bioinf
▴ 10
1
vote
4
replies
475
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 3 days ago
JKim
• 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
15 results • Page
1 of 1
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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