Showing : deseq2 • reset
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 15 minutes ago by 41k • written 15 hours ago by • 0
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60
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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
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57
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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
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1
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59
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 1 day ago by 41k • written 1 day ago by • 0
0
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1
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65
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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 1 day ago by • 0
3
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3
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176
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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 2 days ago by ▴ 10
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3
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175
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 5 days ago by 41k • written 5 days ago by • 0
2
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9
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332
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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
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2
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168
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PCA plot suggestions
DESeq2 PCAtools
updated 4 days ago by 41k • written 6 days ago by • 0
0
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1
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121
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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
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3
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193
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Different Shrunk Log2FC according with reference
DESeq2
updated 7 days ago by 41k • written 7 days ago by ▴ 20
1
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4
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282
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 5 days ago winwater0928 • 0
3
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1
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283
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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
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8
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314
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 6 days ago by ★ 1.3k • written 7 days ago by • 0
3
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3
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206
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by 41k • written 8 days ago by • 0
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1
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116
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rlog transformation
DESeq2
updated 12 days ago by 41k • written 13 days ago by • 0
0
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1
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99
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 12 days ago by 41k • written 13 days ago by • 0
0
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4
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218
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
13 days ago • updated 11 days ago lonn • 0
1
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2
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686
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
13 days ago • updated 4 days ago ussarizona ▴ 10
0
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1
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135
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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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120
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covariate with negative and positive values
DESeq2
updated 12 days ago by 41k • written 14 days ago by • 0
0
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3
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191
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 15 days ago by 41k • written 15 days ago by ▴ 20
0
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4
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252
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DEG with low counts
DESeq2
updated 12 days ago by 41k • written 16 days ago by • 0
0
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1
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121
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Deseq2 Rlog transformation
DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
1
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2
replies
183
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Design Matrix within group comparison more than two groups
DESeq2
18 days ago hemantcnaik • 0
0
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1
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127
views
Bioinformatics student
Des DESeq2
updated 18 days ago by • 0 • written 18 days ago by • 0
0
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1
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167
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DESeq2 gives an error and R crashes
DESeq2
20 days ago • updated 19 days ago Shefali • 0
1
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2
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234
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How to retrieve detailed regression results from deseq2
DESeq2
20 days ago • updated 11 days ago Weiqian ▴ 10
0
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1
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154
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 21 days ago by 41k • written 21 days ago by • 0
0
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2
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154
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 25 days ago by 65k • written 26 days ago by • 0
0
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2
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208
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 days ago by 41k • written 26 days ago by ▴ 30
0
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2
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228
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Regressing out batch effects
DESeq2
updated 21 days ago by 41k • written 26 days ago by • 0
1
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1
reply
159
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DESeq2 - Missing values in count matrix
DESeq2
updated 26 days ago by 65k • written 26 days ago by • 0
1
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6
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414
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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
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1
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145
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
28 days ago Layal • 0
0
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2
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161
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
29 days ago • updated 28 days ago michelafrancesconi8 • 0
0
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4
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243
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 28 days ago by 41k • written 29 days ago by • 0
0
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1
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153
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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
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3
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341
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PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
3
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2
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208
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
0
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1
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165
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collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
1
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2
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226
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
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2
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222
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
0
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3
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255
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Help with Complex DESeq2 Design
DESeq2
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
2
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3
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299
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DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by 41k • written 6 weeks ago by ▴ 20
0
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1
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142
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Help with DESeqDataSetFromHTSeqCount
DESeq2 RSeqAn
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
0
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1
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176
views
lfcShrink error: the line search routine failed
apeglm DESeq2
updated 6 weeks ago by 41k • written 6 weeks ago by • 0
1
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1
reply
172
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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
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2
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216
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With DESeq2 "Not full rank" Error with design
DESeq2 DEs
6 weeks ago feather-W • 0
0
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4
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411
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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
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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
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