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Showing :
DESEq2
•
reset
2
votes
4
replies
125
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
1 day ago • updated 13 hours ago
Shihui
• 0
0
votes
5
replies
123
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2 days ago
Rockbar
• 0
0
votes
3
replies
165
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
4 days ago • updated 3 days ago
ruba-mahmoud
• 0
0
votes
5
replies
139
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2 days ago by
James W. MacDonald
63k • written 3 days ago by
Theo
• 0
1
vote
3
replies
1.3k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 3.5 years ago by
hasse.bossenbroek
• 0
0
votes
4
replies
183
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 6 days ago by
James W. MacDonald
63k • written 7 days ago by
sohail.mbio
▴ 10
1
vote
1
reply
85
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 7 days ago by
James W. MacDonald
63k • written 8 days ago by
Alvin
• 0
0
votes
3
replies
169
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression
DESeq2
updated 10 days ago by
ATpoint
★ 3.4k • written 10 days ago by
xiaowen
• 0
0
votes
3
replies
189
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 9 days ago by
James W. MacDonald
63k • written 11 days ago by
SH
• 0
0
votes
1
reply
102
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 13 days ago by
James W. MacDonald
63k • written 14 days ago by
khaserdene99
• 0
0
votes
1
reply
170
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 14 days ago by
James W. MacDonald
63k • written 14 days ago by
paige.ramkissoon
• 0
1
vote
7
replies
291
views
Permutation test in DESeq2?
DESeq2
updated 13 days ago by
Michael Love
40k • written 15 days ago by
michellewei
• 0
3
votes
3
replies
204
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
16 days ago
Nisha
• 0
3
votes
5
replies
214
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 16 days ago by
ATpoint
★ 3.4k • written 16 days ago by
Shashank
• 0
0
votes
1
reply
102
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 17 days ago by
ATpoint
★ 3.4k • written 17 days ago by
Laura
▴ 10
0
votes
1
reply
87
views
Unable to create ddf object
DESeqDataSetFromMatrix
dds
DESeq2
updated 17 days ago by
James W. MacDonald
63k • written 18 days ago by
naomi.croft
• 0
0
votes
2
replies
153
views
RSubread DESeq2
RNASeqData
DifferentialExpression
DESeq2
19 days ago • updated 18 days ago
Beyza
• 0
0
votes
3
replies
206
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 21 days ago by
James W. MacDonald
63k • written 21 days ago by
jovel_juan
▴ 20
0
votes
1
reply
160
views
Setting up a multi-factor experiement
DESeq2
updated 21 days ago by
Michael Love
40k • written 24 days ago by
john.briseno
• 0
0
votes
1
reply
257
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 21 days ago by
Michael Love
40k • written 27 days ago by
Adam
• 0
0
votes
1
reply
219
views
results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 27 days ago by
James W. MacDonald
63k • written 27 days ago by
Anup
• 0
0
votes
3
replies
714
views
DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 23 days ago by
James W. MacDonald
63k • written 28 days ago by
The_T_cell_Guy
• 0
0
votes
3
replies
249
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 28 days ago by
Alejandro Reyes
★ 1.9k • written 28 days ago by
Alice
• 0
0
votes
1
reply
205
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 29 days ago by
ATpoint
★ 3.4k • written 29 days ago by
Sep
• 0
0
votes
1
reply
148
views
How to properly compare the group-specific samples using DEseq2
DESeq2
updated 29 days ago by
swbarnes2
★ 1.3k • written 29 days ago by
sykbod
• 0
4
votes
13
replies
475
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport
DESeq2
updated 1 day ago by
Michael Love
40k • written 4 weeks ago by
Christian
• 0
0
votes
5
replies
272
views
How to use contrast with multiple treatments?
RNASeqdataanalysis
DESeq2
updated 27 days ago by
swbarnes2
★ 1.3k • written 4 weeks ago by
Sreeja
• 0
2
votes
2
replies
156
views
DESeq2 results - Annotating and exporting results
DESeq2
updated 4 weeks ago by
James W. MacDonald
63k • written 5 weeks ago by
Maka
• 0
3
votes
7
replies
421
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
5 weeks ago • updated 4 weeks ago
casco
▴ 10
0
votes
9
replies
342
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
5 weeks ago • updated 4 weeks ago
mjd275
• 0
1
vote
8
replies
2.1k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 5.6 years ago by
serpalma.v
▴ 60
2
votes
12
replies
515
views
P-value inflation?
DESeq2
updated 4 weeks ago by
James W. MacDonald
63k • written 6 weeks ago by
dsambo
▴ 10
1
vote
2
replies
334
views
DESeq2 batch design
DESeq2
updated 5 weeks ago by
swbarnes2
★ 1.3k • written 6 weeks ago by
Hope
▴ 10
0
votes
1
reply
158
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 5 weeks ago by
ATpoint
★ 3.4k • written 5 weeks ago by
Juan Pablo
• 0
8
votes
15
replies
572
views
PCA percent variance DESeq2
PCA
DESeq2
6 weeks ago • updated 29 days ago
IUH
• 0
1
vote
6
replies
374
views
Time-series RNA-seq analysis using DESeq2
time-series
DESeq2
RNASeq
timecoursedata
TimeCourse
updated 5 weeks ago by
ATpoint
★ 3.4k • written 6 weeks ago by
Debebe
• 0
0
votes
1
reply
182
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
139
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
125
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
310
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 6 weeks ago by
Guido Hooiveld
★ 3.7k • written 6 weeks ago by
Milan
▴ 10
5
votes
2
replies
297
views
can't install DESeq2 ("unable to access index for repository")
biocmanager
DESeq2
6 weeks ago
Alessia
▴ 40
2
votes
5
replies
359
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 6 weeks ago by
Gordon Smyth
48k • written 7 weeks ago by
Sara
• 0
0
votes
1
reply
123
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
164
views
No such file or directory DESeq2
rstudioScRNA
DESeq2
written 7 weeks ago by
DrFizz
• 0
1
vote
3
replies
246
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
185
views
DESeq2 interaction design
DESeq2
updated 7 weeks ago by
Michael Love
40k • written 7 weeks ago by
lamia11me
• 0
0
votes
1
reply
210
views
DESeq2 error after installing BiocManager
scRNAseq
RStudio
DESeq2
updated 7 weeks ago by
ATpoint
★ 3.4k • written 7 weeks ago by
DrFizz
• 0
3
votes
4
replies
386
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
7 weeks ago
Eva
▴ 10
2
votes
4
replies
303
views
DESeq2 "Not full rank" and "Less than full rank" Errors with design ~ time + ind.nested + time:ind.nested
DESeq2
7 weeks ago
Erika
• 0
0
votes
1
reply
167
views
Model matrix not full rank
DESeq2
8 weeks ago • updated 7 weeks ago
isabelle.dupanloup
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar
by
andrew.b.kleist
• 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Comment: Using edgeR and a spike-in to calculate absolute abundance
by
Miguel
• 0
I have the same issue. As far as I understand, many of the approximations to compute differential abundances include normalization steps wh…
Comment: shinyMethyl - saving the file
by
dorota.komar
• 0
ok, it seems that I can embed shinyMethyl as an app in Rmarkdown and it should allow me to keep an interactive character. No idea how to do…
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of
by
Gordon Smyth
48k
The splitOnly option is designed to strictly return split reads, i.e., reads that identify exon junctions rather than simply read-pairs ove…
Votes
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Batch correction and Deseq2
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