Showing : desEQ2 • reset
1
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
updated 1 hour ago by 67k • written 1 day ago by ▴ 30
0
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2
replies
191
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 1 day ago by ★ 4.6k • written 6 days ago by • 0
1
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5
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376
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Deseq2 Design
RNASeq DESeq2
updated 2 days ago by 67k • written 6 days ago by • 0
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5
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339
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p value is 0, padj is 0
DESeq2
6 days ago • updated 5 days ago Wirayatida • 0
1
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2
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384
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
7 days ago • updated 6 days ago georgii.vdovin • 0
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0
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100
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
7 days ago txema.heredia • 0
0
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7
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659
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 7 days ago by • 0 • written 9 days ago by • 0
0
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1
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228
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 11 days ago by 43k • written 12 days ago by ▴ 20
0
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3
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325
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DESeq2 - Comparing Comparisons
DESeq2
updated 7 days ago by 67k • written 14 days ago by • 0
0
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4
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438
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lfcShrink and alpha value
lfcShrink DESeq2
19 days ago • updated 13 days ago cropero • 0
1
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1
reply
217
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 15 days ago by 43k • written 23 days ago by • 0
0
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2
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146
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 15 days ago by 43k • written 16 days ago by • 0
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2
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216
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
21 days ago • updated 20 days ago Anna • 0
1
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2
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504
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Deseq2 res Function
DESeq2
updated 23 days ago by 67k • written 25 days ago by ▴ 10
0
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4
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379
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
26 days ago NB • 0
0
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5
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365
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Identical samples after deseq2 batch effect removal
DESeq2
updated 26 days ago by 43k • written 27 days ago by • 0
0
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1
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213
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 27 days ago by 67k • written 27 days ago by • 0
1
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2
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274
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
28 days ago • updated 27 days ago Denise • 0
0
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1
reply
136
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eRNAs count
RNASeq DESeq2
updated 4 weeks ago by ★ 4.6k • written 4 weeks ago by • 0
0
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1
reply
385
views
DESeq2 rerun returns different results
DESeq2
updated 4 weeks ago by ★ 4.6k • written 4 weeks ago by • 0
0
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1
reply
222
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 4 weeks ago by 43k • written 5 weeks ago by • 0
0
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1
reply
189
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
2
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2
replies
592
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Handling biological replicates in DESeq2
DESeq2
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
5
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2
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25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
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6
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941
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 5 weeks ago by 43k • written 5 weeks ago by ▴ 10
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2
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363
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 6 weeks ago by • 0
4
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5
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613
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
6 weeks ago LuciaNhu • 0
0
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1
reply
382
views
Average expression of genes across replicates
DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
0
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0
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127
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
7 weeks ago info ▴ 10
0
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10
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1.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
7 weeks ago • updated 6 weeks ago Denise • 0
0
votes
1
reply
337
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Deseq to output continous sequencing data
DESeq2
updated 7 weeks ago by 43k • written 9 weeks ago by • 0
1
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4
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800
views
Adjusted p-values become NA when sub-setting samples
DESeq2
9 weeks ago • updated 6 weeks ago txema.heredia • 0
3
votes
3
replies
888
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 7 weeks ago by • 0
0
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2
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348
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 8 weeks ago by • 0
0
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1
reply
286
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
2
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3
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1.0k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
1
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4
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758
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DESeq2 - interactions when using factors concatenated into group
DESeq2
8 weeks ago • updated 7 weeks ago boczniak767 ▴ 740
0
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1
reply
199
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
8 weeks ago JY • 0
0
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1
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286
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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2
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210
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how to extract expression matrix post deseq2
DESeq2
written 9 weeks ago by • 0
0
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2
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208
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Using Normalized Counts in DESeq2
DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
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2
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262
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When running contrasts, does it use normalized read counts?
DESeq2
9 weeks ago Katherine • 0
0
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1
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212
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 9 weeks ago by ★ 1.4k • written 9 weeks ago by • 0
3
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4
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519
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
9 weeks ago Eva ▴ 10
1
vote
4
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503
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 9 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
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1
reply
188
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
3
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11
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753
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 10 weeks ago by • 0
2
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4
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428
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
10 weeks ago jihoon.kim.1495 ▴ 10
0
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6
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832
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 7 weeks ago by 43k • written 10 weeks ago by • 0
5
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4
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462
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
50 results • Page 1 of 1
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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you James, that really helped! I tried CODE `enter code here` but I must have dome it incorrectly, as it showed all in red.
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Please come back to the support site and view your post - I've fixed it for you. If you want to show people your targets file, just paste t…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you Gordon! Apologies if this is a too basic question-I'm a biologist and want to ensure I understand correctly. Here is my metadata …
Comment: nightmare to make custom txdb for genomes from ToxoDB by rohitsatyam102 ▴ 20
I offer my apologies if the title was misleading. I will change it at once. I wrote txdb because the error emnated from `seqlevelsStyle(txd…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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