Showing : DESeq2 • reset
6
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by • 0 • written 4.6 years ago by ▴ 10
9
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12
replies
7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 30
2
votes
9
replies
338
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 6 days ago by 65k • written 6 days ago by • 0
0
votes
8
replies
320
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 7 days ago by ★ 1.3k • written 8 days ago by • 0
0
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7
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400
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DESeq filtering specific to contrasts
DESeq2
updated 12 days ago by 41k • written 10 weeks ago by • 0
1
vote
6
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418
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 28 days ago by • 0
2
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5
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730
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DESeq2 setting significant p-value
DESeq2
updated 12 days ago by 41k • written 5.0 years ago by ▴ 10
2
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5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 14 days ago by • 0 • written 10 months ago by • 0
0
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4
replies
590
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 15 days ago by 41k • written 6 months ago by • 0
0
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4
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257
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DEG with low counts
DESeq2
updated 12 days ago by 41k • written 17 days ago by • 0
0
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4
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250
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by • 0
0
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4
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223
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
14 days ago • updated 12 days ago lonn • 0
1
vote
4
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296
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
1
vote
4
replies
443
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DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 13 hours ago JKim • 0
0
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3
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180
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 hours ago by 41k • written 1 day ago by • 0
3
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3
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209
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
1
vote
3
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199
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Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by 41k • written 8 days ago by ▴ 20
1
vote
3
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184
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
3
replies
198
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by 41k • written 16 days ago by ▴ 20
3
votes
3
replies
191
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 2 days ago by ★ 4.1k • written 3 days ago by ▴ 10
0
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2
replies
179
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PCA plot suggestions
DESeq2 PCAtools
updated 5 days ago by 41k • written 7 days ago by • 0
0
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2
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166
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
29 days ago michelafrancesconi8 • 0
0
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2
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213
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 days ago by 41k • written 26 days ago by ▴ 30
1
vote
2
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689
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago ussarizona ▴ 10
0
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2
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232
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Regressing out batch effects
DESeq2
updated 22 days ago by 41k • written 27 days ago by • 0
1
vote
2
replies
237
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How to retrieve detailed regression results from deseq2
DESeq2
21 days ago • updated 12 days ago Weiqian ▴ 10
1
vote
2
replies
187
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Design Matrix within group comparison more than two groups
DESeq2
19 days ago • updated 18 days ago hemantcnaik • 0
0
votes
2
replies
156
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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
1
reply
156
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 22 days ago by 41k • written 22 days ago by • 0
0
votes
1
reply
101
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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
1
reply
80
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
reply
66
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
1
reply
74
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putting my own expression data in deseq2
DESeq2
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
1
vote
1
reply
74
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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
126
views
covariate with negative and positive values
DESeq2
updated 13 days ago by 41k • written 15 days ago by • 0
1
vote
1
reply
160
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DESeq2 - Missing values in count matrix
DESeq2
updated 27 days ago by 65k • written 27 days ago by • 0
0
votes
1
reply
86
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 12 hours ago by ★ 4.1k • written 12 hours ago by • 0
0
votes
1
reply
119
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rlog transformation
DESeq2
updated 13 days ago by 41k • written 13 days ago by • 0
0
votes
1
reply
125
views
Deseq2 Rlog transformation
DESeq2
updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
3
votes
1
reply
290
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 40
0
votes
1
reply
136
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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
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1
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125
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 days ago by 41k • written 7 days ago by • 0
0
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1
reply
172
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DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago Shefali • 0
0
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1
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129
views
Bioinformatics student
Des DESeq2
updated 19 days ago by • 0 • written 19 days ago by • 0
0
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1
reply
32
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 1 hour ago by ★ 4.1k • written 9 hours ago by • 0
1
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1
reply
148
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
29 days ago Layal • 0
0
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0
replies
18
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Deseq2 and Normalization of RNA sequencing data
DESeq2
9 hours ago kcarey • 0
47 results • Page 1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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