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deseq2
•
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0
votes
0
replies
7
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
59 minutes ago • updated 36 minutes ago
james.zhang20
• 0
0
votes
0
replies
6
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
54 minutes ago • updated 53 minutes ago
kcarey
• 0
0
votes
3
replies
150
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
1
reply
40
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 hours ago by
ATpoint
★ 4.1k • written 3 hours ago by
angelathuynh5
• 0
1
vote
4
replies
428
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 4 hours ago
JKim
• 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
1
vote
1
reply
69
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
62
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Aurora
• 0
0
votes
1
reply
71
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
68
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
180
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 2 days ago by
bioinf
▴ 10
0
votes
2
replies
173
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Aaliya
• 0
1
vote
2
replies
688
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
1
vote
3
replies
178
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
1
vote
4
replies
287
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago
winwater0928
• 0
2
votes
9
replies
333
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
8
replies
316
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
0
votes
1
reply
122
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
196
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
andrebolerbarros
▴ 20
3
votes
1
reply
286
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
3
votes
3
replies
207
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
4
replies
220
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 days ago • updated 11 days ago
lonn
• 0
1
vote
2
replies
235
views
How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago
Weiqian
▴ 10
0
votes
7
replies
398
views
DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
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
0
votes
4
replies
253
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
118
views
rlog transformation
DESeq2
updated 13 days ago by
Michael Love
41k • written 13 days ago by
ishij9717
• 0
0
votes
1
reply
100
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
0
votes
1
reply
121
views
covariate with negative and positive values
DESeq2
updated 13 days ago by
Michael Love
41k • written 15 days ago by
Brynn
• 0
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
0
votes
1
reply
135
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
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
0
votes
4
replies
588
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
0
votes
3
replies
196
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
121
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Sahar
• 0
1
vote
2
replies
184
views
Design Matrix within group comparison more than two groups
DESeq2
19 days ago • updated 18 days ago
hemantcnaik
• 0
0
votes
1
reply
127
views
Bioinformatics student
Des
DESeq2
updated 19 days ago by
hemantcnaik
• 0 • written 19 days ago by
Sahar
• 0
0
votes
1
reply
170
views
DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago
Shefali
• 0
0
votes
2
replies
212
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 21 days ago by
Michael Love
41k • written 26 days ago by
nhaus
▴ 30
0
votes
1
reply
155
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 21 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
0
votes
2
replies
230
views
Regressing out batch effects
DESeq2
updated 21 days ago by
Michael Love
41k • written 27 days ago by
kys91240
• 0
0
votes
2
replies
155
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
159
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
417
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 27 days ago by
Michael Love
41k • written 28 days ago by
RL
• 0
0
votes
2
replies
162
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
29 days ago • updated 28 days ago
michelafrancesconi8
• 0
1
vote
1
reply
146
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago • updated 28 days ago
Layal
• 0
0
votes
4
replies
245
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
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 4 weeks ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
0
votes
1
reply
153
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Mikushi
• 0
1
vote
2
replies
226
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
5 weeks ago
Chanderkant Chaudhary
• 0
50 results • Page
1 of 1
Recent ...
Replies
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…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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