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deseq2
•
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0
votes
0
replies
19
views
Help with Complex DESeq2 Design
DESeq2
14 hours ago
kelsey.beavers
• 0
1
vote
0
replies
40
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
19 hours ago
andrebolerbarros
▴ 30
1
vote
1
reply
67
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Emma
• 0
0
votes
1
reply
38
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 1 day ago by
Michael Love
41k • written 1 day ago by
rahaf.nazzal9
• 0
0
votes
1
reply
45
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Yuqin
• 0
2
votes
2
replies
114
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
4 days ago • updated 2 days ago
feather-W
• 0
0
votes
2
replies
189
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 5 days ago by
Michael Love
41k • written 6 days ago by
gglatzer
• 0
0
votes
4
replies
301
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
Jad
• 0
0
votes
6
replies
254
views
DESeq2 filtering vs edgeR filtering
DESeq2
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
fr8712ca-s
• 0
0
votes
2
replies
126
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
5 days ago • updated 4 days ago
kcarey
• 0
1
vote
1
reply
132
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 days ago by
ATpoint
★ 3.9k • written 7 days ago by
Marilyn
• 0
2
votes
1
reply
153
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 6 days ago by
ATpoint
★ 3.9k • written 7 days ago by
hemantcnaik
• 0
1
vote
1
reply
138
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 8 days ago by
ATpoint
★ 3.9k • written 8 days ago by
synat.keam
• 0
0
votes
3
replies
278
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 6 weeks ago by
pl23
• 0
0
votes
2
replies
245
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
11 days ago • updated 10 days ago
Viktor Thiel
• 0
0
votes
1
reply
110
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2
scCITE-seq
updated 11 days ago by
ATpoint
★ 3.9k • written 11 days ago by
daiane.hemerichbrennan
• 0
0
votes
8
replies
258
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
12 days ago • updated 11 days ago
michelafrancesconi8
• 0
0
votes
1
reply
136
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 12 days ago by
ATpoint
★ 3.9k • written 12 days ago by
Sneha
• 0
1
vote
4
replies
207
views
DESeq2 Replicates
DESeq2
RNASeq
12 days ago
kcarey
• 0
2
votes
6
replies
242
views
Factor vs Character in design
DESeq2
12 days ago
James Aiden
• 0
1
vote
3
replies
228
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
18 days ago • updated 12 days ago
I-Hsuan Lin
▴ 10
4
votes
7
replies
716
views
weird volcano plot
DESeq2
updated 13 days ago by
Shuning
• 0 • written 4 months ago by
shouzheng
▴ 10
0
votes
1
reply
206
views
DEseq2 dispersion plot
DESeq2
updated 13 days ago by
Michael Love
41k • written 19 days ago by
Emma
• 0
1
vote
3
replies
234
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 14 days ago by
swbarnes2
★ 1.3k • written 17 days ago by
sap275
▴ 10
0
votes
2
replies
276
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 16 days ago by
ATpoint
★ 3.9k • written 18 days ago by
Suvi
• 0
0
votes
3
replies
205
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 14 days ago by
James W. MacDonald
65k • written 18 days ago by
MEME
▴ 10
0
votes
1
reply
178
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
zhangaimei
• 0
1
vote
4
replies
249
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
18 days ago • updated 17 days ago
hmillike
• 0
0
votes
1
reply
132
views
few significant genes from DESeq2 analysis
DESeq2
updated 20 days ago by
Michael Love
41k • written 20 days ago by
Ming
• 0
1
vote
3
replies
282
views
DEseq2 coefficient
DESeq2
coefficient
24 days ago • updated 3 days ago
JKim
• 0
3
votes
5
replies
486
views
DESEQ Inquiry
DESeq2
rnaseqGene
RNASeqData
limma
RNASeq
updated 15 days ago by
Michael Love
41k • written 24 days ago by
sap275
▴ 10
2
votes
1
reply
179
views
Limma Question
DESeq2
BatchEffect
limma
RNASeq
updated 22 days ago by
Michael Love
41k • written 22 days ago by
sap275
▴ 10
2
votes
2
replies
230
views
locfunc not found in DESeq2
locfunc
DESeq2
shorth
estimateSizeFactors
24 days ago
Hope
▴ 10
1
vote
2
replies
218
views
evaluate the variable importance on genes
DESeq2
deseq
25 days ago
Meme
• 0
0
votes
3
replies
264
views
library sizes differ extremely after dds
DESeq2
updated 25 days ago by
Michael Love
41k • written 25 days ago by
HAK
• 0
1
vote
4
replies
280
views
Comparing gene expression across three tissue types to identify any difference.
DESeq2
25 days ago
James Aiden
• 0
0
votes
13
replies
531
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 19 days ago by
Michael Love
41k • written 25 days ago by
r.r.bioinf
• 0
1
vote
5
replies
273
views
vst transformation and zero counts
DESeq2
updated 26 days ago by
ATpoint
★ 3.9k • written 26 days ago by
boczniak767
▴ 720
1
vote
12
replies
915
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
26 days ago • updated 20 days ago
paria.alipour
• 0
0
votes
3
replies
226
views
utf-8 codec can't decode byte 0xd5
importr
DESeq2
updated 26 days ago by
Michael Love
41k • written 27 days ago by
yuhang
• 0
0
votes
1
reply
179
views
Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 29 days ago by
ATpoint
★ 3.9k • written 29 days ago by
Aaliya
• 0
0
votes
3
replies
312
views
DESeq2: Adjust for treatment effect patient vs control
DESeq2
updated 27 days ago by
Michael Love
41k • written 4 weeks ago by
Ead72bbe
• 0
0
votes
1
reply
223
views
Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
puffsquash
• 0
0
votes
1
reply
221
views
DESeq filtering specific to contrasts
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Emma
• 0
0
votes
2
replies
387
views
help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
4 weeks ago • updated 19 days ago
ccshao
▴ 70
0
votes
1
reply
210
views
Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Rania Ouaz
• 0
1
vote
2
replies
170
views
DESeq2 issue: can't create DESeq2 object
DESeq2
RBioinf
4 weeks ago
Magdalena
• 0
0
votes
1
reply
128
views
Inconsistency in DESeq2 Log fold change
DESeq2
updated 4 weeks ago by
ATpoint
★ 3.9k • written 4 weeks ago by
Kuldeep
• 0
0
votes
2
replies
211
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2
dese
updated 4 weeks ago by
ATpoint
★ 3.9k • written 4 weeks ago by
Xu
• 0
0
votes
5
replies
352
views
DESEQ2 Repeated Measures-like design error help
DESeq2
updated 27 days ago by
Michael Love
41k • written 5 weeks ago by
DS
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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