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DESEQ2
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1
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
just now
angelathuynh5
• 0
0
votes
1
reply
106
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 hours ago by
Michael Love
41k • written 22 hours ago by
HAK
• 0
1
vote
1
reply
65
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
62
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Aurora
• 0
0
votes
1
reply
71
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
1
reply
67
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
Dev
• 0
3
votes
3
replies
180
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
bioinf
▴ 10
0
votes
2
replies
172
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Aaliya
• 0
1
vote
3
replies
176
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
333
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
0
votes
1
reply
122
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
kcarey
• 0
1
vote
3
replies
195
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by
Michael Love
41k • written 7 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
285
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago
winwater0928
• 0
3
votes
1
reply
286
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 days ago by
Michael Love
41k • written 8 days ago by
i.sudbery
▴ 40
0
votes
8
replies
316
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 6 days ago by
swbarnes2
★ 1.3k • written 8 days ago by
Aaliya
• 0
3
votes
3
replies
207
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
WardDeb
• 0
0
votes
1
reply
118
views
rlog transformation
DESeq2
updated 13 days ago by
Michael Love
41k • written 13 days ago by
ishij9717
• 0
0
votes
1
reply
99
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 13 days ago by
Michael Love
41k • written 13 days ago by
09191919
• 0
1
vote
2
replies
687
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
0
votes
1
reply
120
views
covariate with negative and positive values
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
Brynn
• 0
0
votes
1
reply
135
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
quanah.hudson
• 0
0
votes
4
replies
218
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 days ago • updated 11 days ago
lonn
• 0
0
votes
3
replies
195
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
235
views
How to retrieve detailed regression results from deseq2
DESeq2
20 days ago • updated 12 days ago
Weiqian
▴ 10
0
votes
4
replies
252
views
DEG with low counts
DESeq2
updated 12 days ago by
Michael Love
41k • written 17 days ago by
Rajat
• 0
0
votes
1
reply
121
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Sahar
• 0
1
vote
2
replies
183
views
Design Matrix within group comparison more than two groups
DESeq2
19 days ago • updated 18 days ago
hemantcnaik
• 0
0
votes
1
reply
127
views
Bioinformatics student
Des
DESeq2
updated 19 days ago by
hemantcnaik
• 0 • written 19 days ago by
Sahar
• 0
0
votes
1
reply
169
views
DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago
Shefali
• 0
0
votes
2
replies
211
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 21 days ago by
Michael Love
41k • written 26 days ago by
nhaus
▴ 30
0
votes
1
reply
155
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 21 days ago by
Michael Love
41k • written 22 days ago by
Adelaide
• 0
0
votes
2
replies
229
views
Regressing out batch effects
DESeq2
updated 21 days ago by
Michael Love
41k • written 27 days ago by
kys91240
• 0
0
votes
2
replies
154
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 26 days ago by
James W. MacDonald
65k • written 26 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
159
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Hong Thu
• 0
1
vote
6
replies
415
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 27 days ago by
Michael Love
41k • written 28 days ago by
RL
• 0
1
vote
1
reply
145
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago • updated 28 days ago
Layal
• 0
0
votes
2
replies
162
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
29 days ago • updated 28 days ago
michelafrancesconi8
• 0
0
votes
4
replies
243
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by
Michael Love
41k • written 29 days ago by
Aidan
• 0
0
votes
1
reply
153
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Mikushi
• 0
2
votes
3
replies
343
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Laura
▴ 10
0
votes
1
reply
165
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Léa
• 0
3
votes
2
replies
208
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
5 weeks ago
Anita
▴ 10
1
vote
2
replies
226
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
5 weeks ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
223
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
6 weeks ago • updated 5 weeks ago
kcarey
• 0
2
votes
3
replies
300
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 6 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
255
views
Help with Complex DESeq2 Design
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
kelsey.beavers
• 0
1
vote
1
reply
172
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 6 weeks ago by
Michael Love
41k • written 6 weeks ago by
Emma
• 0
0
votes
1
reply
143
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 6 weeks ago by
Michael Love
41k • written 6 weeks ago by
rahaf.nazzal9
• 0
0
votes
1
reply
179
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 6 weeks ago by
Michael Love
41k • written 6 weeks ago by
Yuqin
• 0
2
votes
2
replies
217
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
6 weeks ago
feather-W
• 0
50 results • Page
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Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Comment: Store output of matchPWM()
by
mat149
▴ 70
out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) Error in do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) : '…
Answer: Store output of matchPWM()
by
James W. MacDonald
65k
Something like this? ``` ind <- as.logical(sapply(hitlist, length)) out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) …
Answer: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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