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Showing :
DESeq2
•
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0
votes
0
replies
21
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
11 hours ago
ar14g12
• 0
1
vote
5
replies
99
views
Mixed up sample info with plotPCA
plotMA
ggplot2
plotPCA
DESeq2
updated 14 hours ago by
Michael Love
40k • written 1 day ago by
sara.jacobson
• 0
0
votes
4
replies
41
views
Extract LRT results for each comparison
LRT
DESeq2
updated 1 day ago by
ATpoint
★ 3.4k • written 1 day ago by
Yijing
• 0
2
votes
4
replies
204
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
6 days ago • updated 5 days ago
Shihui
• 0
0
votes
5
replies
153
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
7 days ago
Rockbar
• 0
0
votes
5
replies
159
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 7 days ago by
James W. MacDonald
63k • written 8 days ago by
Theo
• 0
0
votes
3
replies
187
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE
DESeq2
8 days ago • updated 7 days ago
ruba-mahmoud
• 0
0
votes
4
replies
202
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 11 days ago by
James W. MacDonald
63k • written 11 days ago by
sohail.mbio
▴ 10
1
vote
1
reply
99
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 12 days ago by
James W. MacDonald
63k • written 13 days ago by
Alvin
• 0
0
votes
3
replies
182
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression
DESeq2
updated 15 days ago by
ATpoint
★ 3.4k • written 15 days ago by
xiaowen
• 0
0
votes
3
replies
200
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 14 days ago by
James W. MacDonald
63k • written 15 days ago by
SH
• 0
0
votes
1
reply
110
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 18 days ago by
James W. MacDonald
63k • written 18 days ago by
khaserdene99
• 0
0
votes
1
reply
177
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 19 days ago by
James W. MacDonald
63k • written 19 days ago by
paige.ramkissoon
• 0
1
vote
7
replies
319
views
Permutation test in DESeq2?
DESeq2
updated 18 days ago by
Michael Love
40k • written 20 days ago by
michellewei
• 0
3
votes
3
replies
213
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
20 days ago
Nisha
• 0
3
votes
5
replies
229
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 20 days ago by
ATpoint
★ 3.4k • written 21 days ago by
Shashank
• 0
0
votes
1
reply
108
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 21 days ago by
ATpoint
★ 3.4k • written 21 days ago by
Laura
▴ 10
0
votes
1
reply
96
views
Unable to create ddf object
DESeqDataSetFromMatrix
dds
DESeq2
updated 22 days ago by
James W. MacDonald
63k • written 22 days ago by
naomi.croft
• 0
0
votes
2
replies
159
views
RSubread DESeq2
RNASeqData
DifferentialExpression
DESeq2
24 days ago • updated 22 days ago
Beyza
• 0
0
votes
3
replies
214
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 26 days ago by
James W. MacDonald
63k • written 26 days ago by
jovel_juan
▴ 20
1
vote
2
replies
185
views
Setting up a multi-factor experiement
DESeq2
28 days ago • updated 13 hours ago
john.briseno
• 0
0
votes
1
reply
228
views
results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 4 weeks ago by
James W. MacDonald
63k • written 4 weeks ago by
Anup
• 0
0
votes
1
reply
272
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 26 days ago by
Michael Love
40k • written 4 weeks ago by
Adam
• 0
0
votes
3
replies
750
views
DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 28 days ago by
James W. MacDonald
63k • written 4 weeks ago by
The_T_cell_Guy
• 0
0
votes
3
replies
261
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 4 weeks ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alice
• 0
0
votes
1
reply
215
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 3.4k • written 4 weeks ago by
Sep
• 0
0
votes
1
reply
158
views
How to properly compare the group-specific samples using DEseq2
DESeq2
updated 4 weeks ago by
swbarnes2
★ 1.3k • written 4 weeks ago by
sykbod
• 0
0
votes
5
replies
277
views
How to use contrast with multiple treatments?
RNASeqdataanalysis
DESeq2
updated 4 weeks ago by
swbarnes2
★ 1.3k • written 5 weeks ago by
Sreeja
• 0
4
votes
13
replies
530
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 6 days ago by
Michael Love
40k • written 5 weeks ago by
Christian
• 0
2
votes
2
replies
161
views
DESeq2 results - Annotating and exporting results
DESeq2
updated 5 weeks ago by
James W. MacDonald
63k • written 5 weeks ago by
Maka
• 0
3
votes
7
replies
426
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
5 weeks ago
casco
▴ 10
0
votes
9
replies
354
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
5 weeks ago
mjd275
• 0
0
votes
1
reply
159
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 6 weeks ago by
ATpoint
★ 3.4k • written 6 weeks ago by
Juan Pablo
• 0
8
votes
15
replies
587
views
PCA percent variance DESeq2
PCA
DESeq2
6 weeks ago • updated 4 weeks ago
IUH
• 0
2
votes
12
replies
526
views
P-value inflation?
DESeq2
updated 5 weeks ago by
James W. MacDonald
63k • written 6 weeks ago by
dsambo
▴ 10
1
vote
6
replies
393
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 6 weeks ago by
ATpoint
★ 3.4k • written 6 weeks ago by
Debebe
• 0
0
votes
1
reply
142
views
DEG by deseq2 by Race
DESeq2
updated 6 weeks ago by
Kevin Blighe
3.8k • written 6 weeks ago by
Sharif
• 0
0
votes
1
reply
129
views
the confuse issue in DEseq2 among multi group
DESeq2
updated 6 weeks ago by
James W. MacDonald
63k • written 6 weeks ago by
诗友
• 0
3
votes
2
replies
319
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 7 weeks ago by
Guido Hooiveld
★ 3.7k • written 7 weeks ago by
Milan
▴ 10
5
votes
2
replies
306
views
can't install DESeq2 ("unable to access index for repository")
biocmanager
DESeq2
7 weeks ago • updated 6 weeks ago
Alessia
▴ 40
1
vote
2
replies
347
views
DESeq2 batch design
DESeq2
updated 6 weeks ago by
swbarnes2
★ 1.3k • written 7 weeks ago by
Hope
▴ 10
2
votes
5
replies
364
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 7 weeks ago by
Gordon Smyth
48k • written 7 weeks ago by
Sara
• 0
0
votes
1
reply
132
views
FALSE error when checking a pre made sample data
Rstudio
scRNAseq
DESeq2
updated 7 weeks ago by
ATpoint
★ 3.4k • written 7 weeks ago by
DrFizz
• 0
0
votes
2
replies
165
views
No such file or directory DESeq2
rstudioScRNA
DESeq2
written 7 weeks ago by
DrFizz
• 0
1
vote
3
replies
255
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect
sva
DESeq2
RNASeqData
limma
updated 7 weeks ago by
James W. MacDonald
63k • written 7 weeks ago by
D-Bug
• 0
0
votes
1
reply
187
views
Comparing the effect of single drug and two-drug combination with control in RNA seq data
GeneExpressionWorkflow
DESeq2
updated 6 weeks ago by
Michael Love
40k • written 7 weeks ago by
Kent
• 0
0
votes
1
reply
226
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 8 weeks ago by
ATpoint
★ 3.4k • written 8 weeks ago by
DrFizz
• 0
3
votes
4
replies
406
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
8 weeks ago • updated 7 weeks ago
Eva
▴ 10
2
votes
4
replies
307
views
DESeq2 "Not full rank" and "Less than full rank" Errors with design ~ time + ind.nested + time:ind.nested
DESeq2
8 weeks ago
Erika
• 0
0
votes
1
reply
190
views
DESeq2 interaction design
DESeq2
updated 7 weeks ago by
Michael Love
40k • written 8 weeks ago by
lamia11me
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results
by
James W. MacDonald
63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block()
by
Hervé Pagès
16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences
by
Hervé Pagès
16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results
by
camillab.
▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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James W. MacDonald
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