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DEseq2
•
reset
3
votes
7
replies
3.6k
views
Is it possible to convert "DESeq2's normalized counts" to "DEGs"?
DESeq2
raw
updated 3.0 years ago by
swbarnes2
★ 1.4k • written 3.0 years ago by
Hicham
▴ 10
0
votes
2
replies
1.4k
views
Differentially expression analysis of orthologous genes between two species
DESeq2
tximport
3.0 years ago
Konstantinos
• 0
0
votes
2
replies
809
views
Setting up contrasts within a dataset within conditions (across different genotype) and across conditions (for the same genotype)
DESeq2
3.0 years ago
nrama
• 0
2
votes
3
replies
2.2k
views
Error while reading rsem files in tximport
DESeq2
tximport
rsem
RNASeq
tximportData
3.0 years ago
mohammedtoufiq91
▴ 10
2
votes
1
reply
1.3k
views
How to interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Pratik Mehta
▴ 10
0
votes
2
replies
1.5k
views
Deseq2 and co-expression network normalization
DESeq2
Normalization
DifferentialExpression
r
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
lola
• 0
0
votes
1
reply
743
views
DESeq2, normalization for within-sample comparison, and 3'-end RNAseq data
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
theophile
• 0
4
votes
2
replies
2.2k
views
DESeq2 false positive result?
DESeq2
updated 3.0 years ago by
swbarnes2
★ 1.4k • written 3.0 years ago by
Gregor
▴ 10
1
vote
2
replies
1.4k
views
Changing the sample order in the PCA plot
DESeq2
3.0 years ago
turtle888
• 0
0
votes
2
replies
1.5k
views
Remove low-expressed genes in DESeq2?
DESeq2
lowcountgenes
deseq2
independent
written 3.0 years ago by
erbrocato
• 0
2
votes
4
replies
5.8k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
3.0 years ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
754
views
NA value in padj but only for certain contrasts
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Yiqi
▴ 10
1
vote
12
replies
3.7k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2
edgeR
limma
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Bogdan
▴ 670
0
votes
1
reply
746
views
DESeq2 : Using contrast in results vs performing complete independent analysis
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
andree-anne
• 0
0
votes
2
replies
1.4k
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2
adjp
Volcano
LRT
written 3.0 years ago by
Laia
▴ 10
0
votes
1
reply
1.2k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2
interaction
coefficient
LinearModel
RNASeq
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Pedro Milanez-Almeida
▴ 10
0
votes
1
reply
893
views
Design structure
DESeq2
des
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
Devin
• 0
1
vote
2
replies
1.2k
views
Question about contrasts in DESeq2
DESeq2
3.1 years ago • updated 3.0 years ago
marinaw
▴ 20
0
votes
1
reply
1.1k
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2
time-series
timecoursedata
timecourse
multifactorial
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
arshad1292
• 0
0
votes
1
reply
861
views
Strange dispersion plot with high outliers
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
mary.piper
• 0
0
votes
1
reply
969
views
How to extract DeSeq2 results for the different groups?
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
Itsme
• 0
0
votes
1
reply
844
views
DESeq2 paired multifactor test
DESeq2
StatisticalMethod
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
ijvechetti
▴ 10
1
vote
3
replies
1.7k
views
Problem with DESeq2
DESeq2
apple-m1
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Norbert
▴ 10
0
votes
4
replies
1.5k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
written 3.0 years ago by
James
• 0
0
votes
1
reply
1.7k
views
DESeq2 design function and downstream analyses
DESeq2
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Devin
• 0
0
votes
2
replies
1.3k
views
Filtering normalised counts
DESeq2
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Rob
• 0
0
votes
1
reply
530
views
DESeq2 effect of interaction when using a grouping variable
DESeq2
updated 3.0 years ago by
swbarnes2
★ 1.4k • written 3.0 years ago by
suprun.maria
• 0
1
vote
4
replies
1.1k
views
DESeq2 says my sampleinfo has linear combination error but I don't see it...
DESeq2
updated 3.0 years ago by
Basti
▴ 780 • written 3.0 years ago by
Joon Ho
• 0
1
vote
2
replies
1.4k
views
How to process and analyze Total RNA-Seq data?
DESeq2
R
edgeR
Normalization
RNASeq
3.0 years ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
1.3k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2
RNA-seq
HTseq
DESeqDataSetFromHTSeqCount
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
abhay.kanodia
• 0
0
votes
2
replies
1.5k
views
ChIP-Seq Analysis: Comparing Unannotated Peaks with DESeq2
DESeq2
MACS2
3.0 years ago
vanbelj
▴ 30
0
votes
5
replies
4.8k
views
Error with DESeq2: DESeqDataSet(se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character
DESeq2
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
molly.fraser
• 0
0
votes
1
reply
825
views
Failed Construction of DESEQDataSet Object: C.Elegans
Celegans
DESeq2
dds
Errorinseq_len(length(idx)-1)
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Enzo.Scifo
• 0
0
votes
2
replies
1.4k
views
DESeq2 correction for biological replicate variance using design
DESeq2
3.0 years ago
lukas.krauss
• 0
5
votes
18
replies
9.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 23 months ago by
picasa1983
• 0 • written 3.8 years ago by
Victor
• 0
0
votes
1
reply
1.1k
views
Downstream analysis with Differentially Expressed Genes
DESeq2
GO
goseq
FunctionalAnnotation
updated 3.1 years ago by
Laia
▴ 10 • written 3.1 years ago by
acram
• 0
1
vote
3
replies
2.1k
views
Interpretation of LRT results
DESeq2
LRT
Heatmap
updated 2.2 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Laia
▴ 10
0
votes
2
replies
979
views
Include multiple factors in the DESeq formula design or subset data to analyze
DESeq2
multiple
3.1 years ago
Yijing
• 0
0
votes
6
replies
2.5k
views
How to extract all comparison in DESeq2 LRT test
DESeq2
Likelihood-ratiotest
3.1 years ago
Yijing
• 0
0
votes
13
replies
3.6k
views
DESeq2 design multi factor
DESeq2
design
0substract
nofullrank
updated 3.0 years ago by
Michael Love
43k • written 3.1 years ago by
Laia
▴ 10
0
votes
1
reply
856
views
TOMOseq analysis
DESeq2
tomoda
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Moutaz
• 0
0
votes
2
replies
1.3k
views
RNA-Seq Reads Count
DESeq2
htseq
DEGseq
RNASeq
read
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
CP
• 0
1
vote
3
replies
4.4k
views
DESeq2/genefilter compatibility with R 4.2.2
DESeq2
genefilter
3.1 years ago
Morgane
▴ 10
1
vote
4
replies
1.2k
views
Paired analysis model
DESeq2
3.1 years ago
giulia.lopatriello
• 0
1
vote
1
reply
1.3k
views
Limit the number of nodes in DESeq2
DESeq2
BiocParallel
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Sebastian
▴ 10
2
votes
1
reply
1.1k
views
Different sequencing depth between replicates and samples
DESeq2
edgeR
DiffBind
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
cesar.arenasmena
▴ 10
0
votes
3
replies
2.5k
views
Differential Expression Analysis on RNAseq - RSEM expected_count from UCSC RNA-Seq toil recompute
DESeq2
Toil
RSEM
3.1 years ago
Niveditha
▴ 20
1
vote
4
replies
3.3k
views
plotCounts to visualize variations of a specific genes along conditions
DESeq2
plotCounts
vst
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Laia
▴ 10
3
votes
12
replies
3.5k
views
Replicates in DESeq2
DESeq2
updated 3.1 years ago by
Yijing
• 0 • written 4.3 years ago by
leo.dagata
▴ 10
1
vote
2
replies
1.5k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2
BatchEffect
RNASeq
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
Flavio
• 0
4,839 results • Page
17 of 97
Recent ...
Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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