Showing : DESeq2 • reset
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Handling multiple differential expression comparisons
DESeq2
updated 11 hours ago by 41k • written 2 days ago by ▴ 10
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6
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188
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 1 day ago by ★ 1.3k • written 3 days ago by ▴ 130
2
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3
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150
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 13 hours ago by ★ 4.1k • written 2 days ago by • 0
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2
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91
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DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
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2
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125
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Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 2 days ago kcarey • 0
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3
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129
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 3 days ago by ★ 4.1k • written 4 days ago by • 0
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1
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130
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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 4 days ago by ★ 4.1k • written 4 days ago by • 0
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3
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242
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
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1
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102
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 5 days ago by • 0
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2
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119
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
5 days ago • updated 2 days ago Aurora • 0
0
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1
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100
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
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1
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100
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putting my own expression data in deseq2
DESeq2
updated 5 days ago by ★ 4.1k • written 5 days ago by • 0
3
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3
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223
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 days ago by ★ 4.1k • written 6 days ago by ▴ 10
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2
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204
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PCA plot suggestions
DESeq2 PCAtools
updated 9 days ago by 41k • written 10 days ago by • 0
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3
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214
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 9 days ago by 41k • written 10 days ago by • 0
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9
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388
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 10 days ago by 65k • written 10 days ago by • 0
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1
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151
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 11 days ago by 41k • written 11 days ago by • 0
1
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3
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208
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Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by 41k • written 11 days ago by ▴ 20
1
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4
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319
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago winwater0928 • 0
3
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1
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309
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by 41k • written 12 days ago by ▴ 40
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8
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342
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 10 days ago by ★ 1.3k • written 12 days ago by • 0
3
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3
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227
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by 41k • written 13 days ago by • 0
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1
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136
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rlog transformation
DESeq2
updated 17 days ago by 41k • written 17 days ago by • 0
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1
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112
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 17 days ago by 41k • written 17 days ago by • 0
1
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2
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710
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago ussarizona ▴ 10
0
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1
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133
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covariate with negative and positive values
DESeq2
updated 17 days ago by 41k • written 19 days ago by • 0
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1
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147
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
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4
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235
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 days ago • updated 15 days ago lonn • 0
0
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3
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204
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by 41k • written 20 days ago by ▴ 20
1
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2
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241
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How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago Weiqian ▴ 10
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4
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269
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DEG with low counts
DESeq2
updated 16 days ago by 41k • written 21 days ago by • 0
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1
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130
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Deseq2 Rlog transformation
DESeq2
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
1
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2
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193
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Design Matrix within group comparison more than two groups
DESeq2
23 days ago • updated 22 days ago hemantcnaik • 0
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1
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132
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Bioinformatics student
Des DESeq2
updated 23 days ago by • 0 • written 23 days ago by • 0
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175
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DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago Shefali • 0
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2
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220
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 25 days ago by 41k • written 4 weeks ago by ▴ 30
0
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1
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162
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 25 days ago by 41k • written 26 days ago by • 0
0
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2
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246
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Regressing out batch effects
DESeq2
updated 25 days ago by 41k • written 4 weeks ago by • 0
0
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2
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171
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
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1
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167
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DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
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6
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433
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
1
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1
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156
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
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2
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173
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
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4
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261
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
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1
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160
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
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3
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350
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PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
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1
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170
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collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
3
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2
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215
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
1
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2
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233
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
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2
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229
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
50 results • Page 1 of 1
Recent ...
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Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Comment: fgsea significant result by Chris • 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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