Showing : DeSeq2 • reset
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 24 days ago by • 0 • written 8.8 years ago by ▴ 30
6
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19
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2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 12 days ago by • 0 • written 4.6 years ago by ▴ 10
3
votes
3
replies
254
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 14 days ago by ★ 4.1k • written 14 days ago by ▴ 10
3
votes
1
reply
319
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 days ago by 42k • written 19 days ago by ▴ 40
3
votes
3
replies
235
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
2
votes
5
replies
776
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DESeq2 setting significant p-value
DESeq2
updated 23 days ago by 42k • written 5.0 years ago by ▴ 10
2
votes
3
replies
218
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
2
votes
7
replies
283
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 days ago • updated 1 day ago sajadahmad41454 • 0
2
votes
9
replies
407
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 17 days ago by • 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 25 days ago by • 0 • written 11 months ago by • 0
1
vote
1
reply
139
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 12 days ago by 42k • written 12 days ago by • 0
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 23 days ago Weiqian ▴ 10
1
vote
2
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725
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
25 days ago • updated 16 days ago ussarizona ▴ 10
1
vote
1
reply
152
views
Handling multiple differential expression comparisons
DESeq2
updated 7 days ago by 42k • written 9 days ago by ▴ 10
1
vote
4
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499
views
DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 11 days ago JKim • 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago winwater0928 • 0
1
vote
3
replies
226
views
Different Shrunk Log2FC according with reference
DESeq2
updated 18 days ago by 42k • written 19 days ago by ▴ 20
1
vote
3
replies
238
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 16 days ago by 42k • written 17 days ago by • 0
1
vote
2
replies
206
views
Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago • updated 29 days ago hemantcnaik • 0
1
vote
3
replies
274
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
1
reply
139
views
covariate with negative and positive values
DESeq2
updated 24 days ago by 42k • written 26 days ago by • 0
0
votes
4
replies
613
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 26 days ago by 42k • written 6 months ago by • 0
0
votes
1
reply
138
views
Deseq2 Rlog transformation
DESeq2
updated 27 days ago by ★ 4.1k • written 29 days ago by • 0
0
votes
6
replies
253
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 days ago by ★ 1.4k • written 10 days ago by ▴ 130
0
votes
3
replies
279
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by 42k • written 12 days ago by • 0
0
votes
1
reply
70
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
8
replies
363
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 18 days ago by ★ 1.4k • written 19 days ago by • 0
0
votes
1
reply
162
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
2
replies
219
views
PCA plot suggestions
DESeq2 PCAtools
updated 16 days ago by 42k • written 18 days ago by • 0
0
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7
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436
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DESeq filtering specific to contrasts
DESeq2
updated 23 days ago by 42k • written 12 weeks ago by • 0
0
votes
2
replies
183
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago kcarey • 0
0
votes
3
replies
213
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 26 days ago by 42k • written 27 days ago by ▴ 20
0
votes
3
replies
186
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 10 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
2
replies
138
views
DESeq2 v1.35.0
DESeq2
updated 10 days ago by 42k • written 10 days ago by • 0
0
votes
1
reply
123
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 12 days ago by 42k • written 13 days ago by • 0
0
votes
4
replies
280
views
DEG with low counts
DESeq2
updated 23 days ago by 42k • written 28 days ago by • 0
0
votes
2
replies
148
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
13 days ago • updated 10 days ago Aurora • 0
0
votes
1
reply
125
views
putting my own expression data in deseq2
DESeq2
updated 12 days ago by ★ 4.1k • written 13 days ago by • 0
0
votes
1
reply
119
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 24 days ago by 42k • written 25 days ago by • 0
0
votes
1
reply
144
views
rlog transformation
DESeq2
updated 24 days ago by 42k • written 24 days ago by • 0
0
votes
1
reply
76
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
0
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4
replies
248
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
25 days ago • updated 23 days ago lonn • 0
0
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1
reply
157
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 24 days ago by ★ 4.1k • written 25 days ago by • 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 2 days ago by • 0 • written 15 months ago by ▴ 10
44 results • Page 1 of 1
Recent ...
Replies
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Comment: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by zzrammal • 0
thank you for your response. The problem is resolved. When i did a fit for the linear model i put NULL for the design fit <- lmFit(count_…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont by Denis • 0
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Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: minfi latest update for EPIC V2 chip
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
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