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DESeq2
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0
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0
replies
16
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 hours ago
lonn
• 0
0
votes
0
replies
26
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 hours ago • updated 15 hours ago
ussarizona
• 0
0
votes
0
replies
28
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
18 hours ago
quanah.hudson
• 0
0
votes
0
replies
42
views
covariate with negative and positive values
DESeq2
1 day ago
Brynn
• 0
0
votes
3
replies
128
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
158
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
0
votes
1
reply
83
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 0
1
vote
2
replies
145
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago
hemantcnaik
• 0
0
votes
1
reply
100
views
Bioinformatics student
Des
DESeq2
updated 5 days ago by
hemantcnaik
• 0 • written 5 days ago by
Sahar
• 0
0
votes
1
reply
138
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
1
vote
1
reply
153
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
0
votes
1
reply
120
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
Adelaide
• 0
0
votes
2
replies
127
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
joshua.mannheimer
• 0
0
votes
2
replies
175
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
41k • written 12 days ago by
nhaus
▴ 30
0
votes
2
replies
210
views
Regressing out batch effects
DESeq2
updated 8 days ago by
Michael Love
41k • written 13 days ago by
kys91240
• 0
1
vote
1
reply
143
views
DESeq2 - Missing values in count matrix
DESeq2
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Hong Thu
• 0
1
vote
6
replies
388
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 14 days ago by
Michael Love
41k • written 14 days ago by
RL
• 0
1
vote
1
reply
125
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
15 days ago • updated 14 days ago
Layal
• 0
0
votes
2
replies
139
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
15 days ago • updated 14 days ago
michelafrancesconi8
• 0
0
votes
4
replies
209
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
Aidan
• 0
0
votes
1
reply
130
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 20 days ago by
Michael Love
41k • written 20 days ago by
Mikushi
• 0
2
votes
3
replies
309
views
PCA of different bacterial species
DESeq2
updated 21 days ago by
Michael Love
41k • written 22 days ago by
Laura
▴ 10
3
votes
2
replies
186
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
23 days ago
Anita
▴ 10
0
votes
1
reply
146
views
collapseReplicates dimension error
DESeq2
Dese
updated 23 days ago by
Michael Love
41k • written 26 days ago by
Léa
• 0
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
27 days ago • updated 21 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
194
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
28 days ago • updated 27 days ago
kcarey
• 0
0
votes
3
replies
223
views
Help with Complex DESeq2 Design
DESeq2
updated 28 days ago by
ATpoint
★ 4.0k • written 4 weeks ago by
kelsey.beavers
• 0
2
votes
3
replies
267
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 28 days ago by
Michael Love
41k • written 4 weeks ago by
andrebolerbarros
▴ 20
0
votes
1
reply
125
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
rahaf.nazzal9
• 0
0
votes
1
reply
157
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Yuqin
• 0
1
vote
1
reply
154
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Emma
• 0
2
votes
2
replies
196
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
4 weeks ago
feather-W
• 0
0
votes
4
replies
396
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
Jad
• 0
0
votes
2
replies
223
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 weeks ago • updated 4 weeks ago
kcarey
• 0
0
votes
7
replies
394
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 22 days ago
fr8712ca-s
• 0
0
votes
2
replies
289
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
gglatzer
• 0
2
votes
1
reply
219
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
hemantcnaik
• 0
1
vote
1
reply
196
views
i'm not getting any differentially expressed genes.
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
Marilyn
• 0
1
vote
1
reply
190
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
synat.keam
• 0
0
votes
2
replies
311
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
5 weeks ago
Viktor Thiel
• 0
0
votes
1
reply
193
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
daiane.hemerichbrennan
• 0
0
votes
8
replies
362
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
5 weeks ago
michelafrancesconi8
• 0
0
votes
1
reply
196
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
Sneha
• 0
1
vote
4
replies
279
views
DESeq2 Replicates
DESeq2
RNASeq
6 weeks ago
kcarey
• 0
2
votes
6
replies
307
views
Factor vs Character in design
DESeq2
6 weeks ago
James Aiden
• 0
1
vote
3
replies
327
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 6 weeks ago by
swbarnes2
★ 1.3k • written 6 weeks ago by
sap275
▴ 10
0
votes
3
replies
274
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
MEME
▴ 10
0
votes
1
reply
226
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
zhangaimei
• 0
1
vote
4
replies
309
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
6 weeks ago
hmillike
• 0
0
votes
2
replies
346
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
Suvi
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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