Showing : DESEQ2 • reset
0
votes
1
reply
79
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 hours ago by 41k • written 18 hours ago by • 0
1
vote
1
reply
61
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
1
reply
57
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
0
votes
1
reply
59
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
1
reply
69
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
3
votes
3
replies
178
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 2 days ago by ★ 4.1k • written 2 days ago by ▴ 10
1
vote
3
replies
175
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 5 days ago by 41k • written 5 days ago by • 0
2
votes
9
replies
332
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 5 days ago by 65k • written 6 days ago by • 0
0
votes
2
replies
169
views
PCA plot suggestions
DESeq2 PCAtools
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
121
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 6 days ago by 41k • written 6 days ago by • 0
1
vote
3
replies
194
views
Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by 41k • written 7 days ago by ▴ 20
1
vote
4
replies
283
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
284
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 days ago by 41k • written 7 days ago by ▴ 40
0
votes
8
replies
315
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 6 days ago by ★ 1.3k • written 8 days ago by • 0
3
votes
3
replies
206
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
0
votes
1
reply
117
views
rlog transformation
DESeq2
updated 13 days ago by 41k • written 13 days ago by • 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 41k • written 13 days ago by • 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
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
135
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 13 days ago by ★ 4.1k • written 14 days ago by • 0
0
votes
1
reply
120
views
covariate with negative and positive values
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
0
votes
3
replies
192
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by 41k • written 16 days ago by ▴ 20
0
votes
4
replies
252
views
DEG with low counts
DESeq2
updated 12 days ago by 41k • written 16 days ago by • 0
0
votes
1
reply
121
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 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 • 0 • written 19 days ago by • 0
0
votes
1
reply
169
views
DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago Shefali • 0
1
vote
2
replies
235
views
How to retrieve detailed regression results from deseq2
DESeq2
20 days ago • updated 11 days ago Weiqian ▴ 10
0
votes
1
reply
154
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 21 days ago by 41k • written 22 days ago by • 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 65k • written 26 days ago by • 0
0
votes
2
replies
208
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 days ago by 41k • written 26 days ago by ▴ 30
0
votes
2
replies
228
views
Regressing out batch effects
DESeq2
updated 21 days ago by 41k • written 27 days ago by • 0
1
vote
1
reply
159
views
DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by 65k • written 27 days ago by • 0
1
vote
6
replies
414
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 27 days ago by 41k • written 27 days ago by • 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
161
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 28 days ago by 41k • written 29 days ago by • 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 41k • written 4 weeks ago by • 0
2
votes
3
replies
341
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
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
0
votes
1
reply
165
views
collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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
5 weeks ago kcarey • 0
0
votes
3
replies
255
views
Help with Complex DESeq2 Design
DESeq2
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
2
votes
3
replies
299
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 6 weeks ago by ▴ 20
0
votes
1
reply
142
views
Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
0
votes
1
reply
177
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 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 41k • written 6 weeks ago by • 0
2
votes
2
replies
216
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
6 weeks ago feather-W • 0
0
votes
4
replies
412
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
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…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
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
Awards • All
Popular Question to Ian D. ▴ 70
Popular Question to junhui.li11 • 0
Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
Centurion to Chris • 0
Locations • All
United States, 2 minutes ago
United States, 4 minutes ago
Worcester, 15 minutes ago
Italy, 31 minutes ago
India, 1 hour ago
Traffic: 652 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6