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DESeq2
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0
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replies
16
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
9 hours ago • updated 8 hours ago
kcarey
• 0
0
votes
1
reply
27
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 6 minutes ago by
ATpoint
★ 4.1k • written 9 hours ago by
james.zhang20
• 0
0
votes
1
reply
85
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 11 hours ago by
ATpoint
★ 4.1k • written 11 hours ago by
angelathuynh5
• 0
0
votes
3
replies
173
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 10 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
1
vote
1
reply
73
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
65
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
0
votes
1
reply
78
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
1
reply
72
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
Dev
• 0
3
votes
3
replies
189
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
0
votes
2
replies
178
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
3
replies
183
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
337
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
0
votes
1
reply
124
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
1
vote
3
replies
198
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
295
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 6 days ago
winwater0928
• 0
3
votes
1
reply
289
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
0
votes
8
replies
319
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
3
votes
3
replies
208
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
WardDeb
• 0
0
votes
1
reply
119
views
rlog transformation
DESeq2
updated 13 days ago by
Michael Love
41k • written 13 days ago by
ishij9717
• 0
0
votes
1
reply
101
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 13 days ago by
Michael Love
41k • written 13 days ago by
09191919
• 0
1
vote
2
replies
689
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
0
votes
1
reply
126
views
covariate with negative and positive values
DESeq2
updated 13 days ago by
Michael Love
41k • written 15 days ago by
Brynn
• 0
0
votes
1
reply
136
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
quanah.hudson
• 0
0
votes
4
replies
223
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 days ago • updated 12 days ago
lonn
• 0
0
votes
3
replies
198
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
237
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago
Weiqian
▴ 10
0
votes
4
replies
257
views
DEG with low counts
DESeq2
updated 12 days ago by
Michael Love
41k • written 17 days ago by
Rajat
• 0
0
votes
1
reply
125
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
1
vote
2
replies
187
views
Design Matrix within group comparison more than two groups
DESeq2
19 days ago • updated 18 days ago
hemantcnaik
• 0
0
votes
1
reply
129
views
Bioinformatics student
Des
DESeq2
updated 19 days ago by
hemantcnaik
• 0 • written 19 days ago by
Sahar
• 0
0
votes
1
reply
172
views
DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago
Shefali
• 0
0
votes
2
replies
213
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 22 days ago by
Michael Love
41k • written 26 days ago by
nhaus
▴ 30
0
votes
1
reply
156
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 22 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
0
votes
2
replies
232
views
Regressing out batch effects
DESeq2
updated 22 days ago by
Michael Love
41k • written 27 days ago by
kys91240
• 0
0
votes
2
replies
156
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Hong Thu
• 0
1
vote
6
replies
418
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 28 days ago by
Michael Love
41k • written 28 days ago by
RL
• 0
1
vote
1
reply
148
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago • updated 28 days ago
Layal
• 0
0
votes
2
replies
166
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
29 days ago • updated 28 days ago
michelafrancesconi8
• 0
0
votes
4
replies
250
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
1
vote
4
replies
440
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 13 hours ago
JKim
• 0
0
votes
7
replies
400
views
DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
4
replies
590
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 15 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 14 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
6
votes
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 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
730
views
DESeq2 setting significant p-value
DESeq2
updated 12 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 13 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
47 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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