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DESeq2
•
reset
0
votes
0
replies
62
views
Plot PCA with ellipses using ggplot
DESeq2
ggplot
PCA
7 hours ago
robledoj13
• 0
3
votes
5
replies
291
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
2 days ago • updated 1 day ago
MedocRafael
• 0
4
votes
2
replies
714
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
8 days ago • updated 2 days ago
mila
▴ 10
0
votes
0
replies
170
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2
volcanoplot
LRT
2 days ago
Eric
• 0
0
votes
3
replies
278
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.2k • written 3 days ago by
Mark
• 0
1
vote
3
replies
304
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 4 days ago by
Michael Love
42k • written 6 days ago by
picasa1983
• 0
0
votes
10
replies
628
views
Two treatments, one control
DESeq2
stageR
17 days ago • updated 4 days ago
alephreish
• 0
3
votes
8
replies
24k
views
Deseq: What does "BaseMean" mean?
deseq2
written 5.9 years ago by
183227851
• 0
0
votes
2
replies
733
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
7 days ago • updated 4 days ago
Fiona
• 0
2
votes
3
replies
263
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2
R
written 8 days ago by
tbiewerh
• 0
0
votes
1
reply
122
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 8 days ago by
ATpoint
★ 4.2k • written 8 days ago by
picasa1983
• 0
0
votes
0
replies
117
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
9 days ago
smac_head
• 0
4
votes
12
replies
534
views
DGE with a Continuous Variable
DESeq2
model
updated 18 hours ago by
Michael Love
42k • written 10 days ago by
picasa1983
• 0
1
vote
2
replies
322
views
DESeq2: two conditions two genotypes
DESeq2
15 days ago • updated 12 days ago
Rocio
• 0
2
votes
3
replies
377
views
DESeq normalized counts vs CQN and statistics
DESeq2
cqn
updated 11 days ago by
Michael Love
42k • written 15 days ago by
emlucero
• 0
0
votes
1
reply
212
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 16 days ago by
Michael Love
42k • written 19 days ago by
Ειρήνη
• 0
0
votes
1
reply
149
views
unreal negative log2fc values
DESeq2
des
updated 21 days ago by
James W. MacDonald
66k • written 21 days ago by
Atul K.
• 0
0
votes
0
replies
153
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
23 days ago
BioinfGuru
▴ 30
0
votes
1
reply
224
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 23 days ago by
Michael Love
42k • written 24 days ago by
K
• 0
1
vote
8
replies
482
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 18 days ago by
Gordon Smyth
51k • written 4 weeks ago by
Alec
• 0
1
vote
5
replies
386
views
DESeq2 ML Query
DESeq2
updated 10 days ago by
Michael Love
42k • written 5 weeks ago by
chris2.a.white
• 0
1
vote
8
replies
3.1k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.4 years ago by
serpalma.v
▴ 60
2
votes
1
reply
664
views
DESeq2 time course using fitted splines
RNASeqData
TimeCourse
DESeq2
timecoursedata
updated 28 days ago by
Michael Love
42k • written 12 months ago by
georgii.vdovin
• 0
2
votes
3
replies
4.1k
views
Deseq2 use fpkm
deseq2
updated 29 days ago by
Michael Love
42k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
24 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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