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Deseq2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 6 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
16
replies
2.2k
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
Michael Love
41k • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
695
views
DESeq2 setting significant p-value
DESeq2
updated 5 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
0
votes
7
replies
386
views
DESeq filtering specific to contrasts
DESeq2
updated 5 days ago by
Michael Love
41k • written 9 weeks ago by
Emma
• 0
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
1
vote
2
replies
219
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
0
votes
8
replies
217
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 8 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 5 days ago
lonn
• 0
3
votes
1
reply
165
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
3
votes
3
replies
156
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
0
votes
1
reply
113
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
3
replies
100
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 57 minutes ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
0
votes
1
reply
97
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
ussarizona
• 0
0
votes
1
reply
89
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
1
vote
3
replies
84
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
1
reply
70
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 17 hours ago by
Michael Love
41k • written 20 hours ago by
kcarey
• 0
0
votes
2
replies
33
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 46 minutes ago by
James W. MacDonald
65k • written 1 hour ago by
Alexandre
• 0
0
votes
1
reply
24
views
PCA plot suggestions
DESeq2
PCAtools
updated just now by
JKim
• 0 • written 10 hours ago by
Aaliya
• 0
19 results • Page
1 of 1
Recent ...
Replies
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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