Showing : DESeq2 • reset
9
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12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 18 days ago by • 0 • written 8.8 years ago by ▴ 30
6
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19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 6 days ago by • 0 • written 4.6 years ago by ▴ 10
3
votes
3
replies
228
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by 41k • written 14 days ago by • 0
3
votes
3
replies
235
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 7 days ago by ★ 4.1k • written 7 days ago by ▴ 10
3
votes
1
reply
315
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 12 days ago by 41k • written 13 days ago by ▴ 40
2
votes
5
replies
753
views
DESeq2 setting significant p-value
DESeq2
updated 17 days ago by 41k • written 5.0 years ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 days ago by • 0 • written 10 months ago by • 0
2
votes
3
replies
171
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by ★ 4.1k • written 3 days ago by • 0
2
votes
9
replies
392
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 11 days ago by 65k • written 11 days ago by • 0
1
vote
4
replies
481
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 5 days ago JKim • 0
1
vote
1
reply
109
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 6 days ago by 41k • written 6 days ago by • 0
1
vote
4
replies
328
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
12 days ago • updated 10 days ago winwater0928 • 0
1
vote
3
replies
215
views
Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by 41k • written 12 days ago by ▴ 20
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
26 days ago • updated 17 days ago Weiqian ▴ 10
1
vote
3
replies
221
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 10 days ago by 41k • written 11 days ago by • 0
1
vote
2
replies
197
views
Design Matrix within group comparison more than two groups
DESeq2
24 days ago • updated 23 days ago hemantcnaik • 0
1
vote
1
reply
99
views
Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by 41k • written 3 days ago by ▴ 10
1
vote
2
replies
714
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 days ago • updated 10 days ago ussarizona ▴ 10
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by 41k • written 21 days ago by ▴ 20
0
votes
1
reply
165
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 27 days ago by 41k • written 27 days ago by • 0
0
votes
1
reply
103
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
2
replies
122
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
6 days ago • updated 3 days ago Aurora • 0
0
votes
1
reply
110
views
putting my own expression data in deseq2
DESeq2
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
2
replies
223
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 26 days ago by 41k • written 4 weeks ago by ▴ 30
0
votes
3
replies
252
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
1
reply
142
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 5 days ago by • 0
0
votes
2
replies
137
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
5 days ago • updated 4 days ago kcarey • 0
0
votes
3
replies
136
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 days ago by ★ 4.1k • written 5 days ago by • 0
0
votes
1
reply
132
views
Deseq2 Rlog transformation
DESeq2
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 17 days ago by 41k • written 22 days ago by • 0
0
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2
replies
107
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
7
replies
423
views
DESeq filtering specific to contrasts
DESeq2
updated 17 days ago by 41k • written 11 weeks ago by • 0
0
votes
6
replies
213
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 2 days ago by ★ 1.3k • written 4 days ago by ▴ 130
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 18 days ago by 41k • written 20 days ago by • 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago Shefali • 0
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
4
replies
238
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
19 days ago • updated 16 days ago lonn • 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 18 days ago by 41k • written 18 days ago by • 0
0
votes
1
reply
137
views
rlog transformation
DESeq2
updated 18 days ago by 41k • written 18 days ago by • 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 27 days ago by 41k • written 4 weeks ago by • 0
0
votes
4
replies
602
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 20 days ago by 41k • written 6 months ago by • 0
0
votes
8
replies
349
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 days ago by ★ 1.3k • written 13 days ago by • 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 12 days ago by 41k • written 12 days ago by • 0
0
votes
2
replies
210
views
PCA plot suggestions
DESeq2 PCAtools
updated 10 days ago by 41k • written 11 days ago by • 0
0
votes
1
reply
134
views
Bioinformatics student
Des DESeq2
updated 24 days ago by • 0 • written 24 days ago by • 0
45 results • Page 1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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