Showing : DESEQ2 • reset
3
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2 minutes ago by 47k • written 1 day ago by ▴ 10
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44
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
2 days ago Fred • 0
1
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2
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136
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Normalized counts from LRT or Wald test?
DESeq2
updated 2 days ago by ★ 2.9k • written 3 days ago by • 0
2
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1
reply
118
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DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 4 days ago by ★ 2.9k • written 4 days ago by • 0
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0
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38
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Genes with highest differential expression have very low read counts for most genes
RNASeq depmap DESeq2
5 days ago • updated 18 hours ago Ben • 0
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0
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43
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WGCNA of two different cohorts study
Combat DESeq2 edgeR DifferentialExpression WGCNA
6 days ago • updated 23 hours ago suphamon.j • 0
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2
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94
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DoparParam() execution fails when foreach() works
clustermq doparallel DESeq2
7 days ago • updated 6 days ago boris • 0
0
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2
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85
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Nanostring data differential expression analysis: limma or DESeq2?
DESeq2 NanoStringDiff limma
7 days ago pg45863 • 0
0
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1
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59
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how to solve this error
DESeq2 GEO miRNAData
updated 7 days ago by ★ 2.9k • written 7 days ago by • 0
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4
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179
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
8 days ago sreeshmaraj72 • 0
0
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1
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120
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 7 days ago by ★ 1.2k • written 8 days ago by • 0
1
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9
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3.9k
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how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 5.2 years ago by • 0
1
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3
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211
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Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 13 days ago by ★ 1.2k • written 14 days ago by • 0
1
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2
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275
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Batch effect between biological replicates
BatchEffect DESeq2
16 days ago • updated 13 days ago gtechbio ▴ 10
1
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3
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247
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Find if one gene has a significantly different Log2FC than a different gene
DESeq2
updated 9 days ago by 40k • written 16 days ago by • 0
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3
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292
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Dispersion outliers genes
Dispersion DESeq2
15 days ago • updated 10 days ago raya.fai ▴ 60
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1
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104
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Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 15 days ago by 63k • written 15 days ago by • 0
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2
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803
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about baseMean in DEseq2
DESeq2
written 22 months ago by ▴ 660
3
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3
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382
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Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 5 months ago by • 0
0
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2
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205
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Accounting for technical replicates in DESeq2
DESeq2
updated 18 days ago by ★ 1.2k • written 18 days ago by • 0
3
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1
reply
170
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Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 20 days ago by 40k • written 20 days ago by • 0
2
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1
reply
124
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scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 21 days ago by 40k • written 21 days ago by • 0
2
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7
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497
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optimHess problem in apeglm/DESeq2
DESeq2 apeglm
updated 19 days ago by 40k • written 21 days ago by ★ 2.9k
1
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2
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153
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Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue Spati RSEM deno DEseq2
21 days ago • updated 20 days ago shashank • 0
1
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2
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136
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 21 days ago by 47k • written 21 days ago by • 0
0
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1
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138
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DESeq2: Comparison between 1 test sample with 1 control sample
DESeq2
updated 22 days ago by ★ 2.9k • written 22 days ago by • 0
2
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17
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574
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lfcshrink error DESeq2
DESeq2 lfcshrink DESe
updated 19 days ago by 40k • written 22 days ago by • 0
0
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2
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190
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Deseq2 design
DESeq2 genes Differential expressed
22 days ago • updated 18 days ago Syed Zaheer ▴ 10
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2
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159
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 26 days ago by • 0
0
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2
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274
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
23 days ago António Miguel de Jesus Domingues ▴ 490
0
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3
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260
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DESeq2 1.40.0 binary install issue on Mac M1 (Bioconductor 3.17)
DESeq2
written 28 days ago by ▴ 10
0
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3
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253
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Can i perform DEseq2 from 2 different rse objects download from RECOUNT database
DESeq2 recount GTEx TCGA recount3
updated 27 days ago by ★ 2.9k • written 28 days ago by ▴ 20
2
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2
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165
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load failed for ‘DESeq2’
DESeq2
updated 28 days ago by 3.5k • written 28 days ago by ▴ 10
8
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12
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733
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DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 19 days ago by 40k • written 4 weeks ago by ▴ 90
0
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2
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165
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model matrix not full rank
DESeq2 RNASeq
updated 27 days ago by • 0 • written 4 weeks ago by • 0
0
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2
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161
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ANOVA-like testing for bulkRNAseq with three conditions with Wald test
DESeq2
updated 4 weeks ago by ★ 2.9k • written 4 weeks ago by • 0
0
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1
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158
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calculating effect of condition taking into account patient origin and clone_origin
DESeq2
updated 4 weeks ago by 40k • written 5 weeks ago by • 0
1
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2
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190
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Wondering if DESeq2 is appropriate for PhIP-seq data?
DESeq2 PhIP-seq
5 weeks ago • updated 10 days ago Samantha • 0
0
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1
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152
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What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 4 weeks ago by 40k • written 6 weeks ago by • 0
0
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1
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169
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DESeq2 Results and Alpha questions
DESeq2
updated 4 weeks ago by 40k • written 4 weeks ago by • 0
1
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2
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181
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Different regions for normalisation
DESeq2 median-of-ratios normalisation
4 weeks ago msrch • 0
0
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2
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176
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
5 weeks ago • updated 4 weeks ago paria.alipour • 0
0
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1
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141
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Performing pair-wise comparisons for smaller p value analyzing time series data using deseq2
DESeq2
updated 4 weeks ago by ★ 2.9k • written 5 weeks ago by • 0
0
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1
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165
views
DESeq2 design formula
DESeq2
updated 5 weeks ago by ★ 1.2k • written 5 weeks ago by • 0
1
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4
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400
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Merging samples from different sequencing runs
DESeq2
9 weeks ago • updated 5 days ago Zainab • 0
0
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2
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202
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GenomicRanges coult not be loaded after R upgrade
DESeq2 Bioconductor GenomicRanges
updated 27 days ago by • 0 • written 5 weeks ago by • 0
7
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8
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8.5k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 5 weeks ago by ★ 2.9k • written 6.8 years ago by ▴ 10
1
vote
1
reply
194
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 5 weeks ago by 47k • written 5 weeks ago by • 0
1
vote
1
reply
170
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RNA-seq data collected at differnt time points
DESeq2
updated 5 weeks ago by ★ 2.9k • written 5 weeks ago by • 0
0
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3
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196
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remving pseudogenes and lncRNA from deseq2 res
filter deseq2
updated 4 weeks ago by 40k • written 5 weeks ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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