Showing : DESEQ2 • reset
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2 lowcount
updated 3 months ago by • 0 • written 9.2 years ago by ▴ 40
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
14
votes
5
replies
22k
views
Dealing with genes that have Padj=NA
deseq2
updated 9 months ago by • 0 • written 8.4 years ago by ▴ 60
13
votes
22
replies
27k
views
DESEq2 Paired samples Before and after treatment
deseq2 paired samples
updated 9 weeks ago by 41k • written 7.9 years ago by ▴ 30
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
8
votes
8
replies
9.8k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 7 months ago by • 0 • written 4.8 years ago by ▴ 40
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 18 months ago by ▴ 20
8
votes
15
replies
1.5k
views
PCA percent variance DESeq2
PCA DESeq2
8 months ago IUH • 0
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by 41k • written 12 months ago by ▴ 90
7
votes
4
replies
2.7k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 3 months ago by • 0 • written 6.2 years ago by ▴ 20
7
votes
3
replies
872
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 9 months ago by 41k • written 9 months ago by ▴ 20
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by • 0 • written 4.6 years ago by ▴ 10
6
votes
11
replies
4.0k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 7 weeks ago by • 0 • written 3.2 years ago by ▴ 40
6
votes
5
replies
4.1k
views
DESeq2: Extremely low pvalues
deseq2
updated 10 months ago by 65k • written 7.8 years ago by ▴ 20
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq deseq2
updated 9 months ago by • 0 • written 9.3 years ago by ▴ 40
5
votes
2
replies
863
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
8 months ago Alessia ▴ 40
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.3 years ago by • 0
4
votes
7
replies
694
views
DESeq2 unable to handle large count values
DESeq2
updated 6 weeks ago by 41k • written 5 months ago by • 0
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 0
4
votes
7
replies
856
views
weird volcano plot
DESeq2
updated 8 weeks ago by • 0 • written 5 months ago by ▴ 10
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 6 weeks ago by • 0 • written 12 months ago by ▴ 10
4
votes
6
replies
2.3k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 11 months ago by 41k • written 12 months ago by • 0
3
votes
3
replies
975
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 17 months ago by • 0
3
votes
6
replies
2.7k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 9 weeks ago by • 0 • written 5.2 years ago by ▴ 50
3
votes
12
replies
2.1k
views
t.test to determine the P-value in DESeq2
DESeq2
written 18 months ago by • 0
3
votes
2
replies
669
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
5
replies
858
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 6 months ago by 41k • written 6 months ago by • 0
3
votes
6
replies
836
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by • 0 • written 5.6 years ago by • 0
3
votes
3
replies
207
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 8 days ago by 41k • written 9 days ago by • 0
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 10 months ago by • 0
3
votes
1
reply
619
views
Applying DESeq2 to (suspected) Poisson distributed gene expression data (in the case of pseudoreplication)
DESeq2
updated 11 months ago by 41k • written 11 months ago by • 0
3
votes
3
replies
947
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
3
votes
5
replies
613
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
3
votes
2
replies
344
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 12 weeks ago by ▴ 30 • written 12 weeks ago by • 0
3
votes
2
replies
1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
3
votes
16
replies
2.1k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 3 months ago by 3.8k • written 2.8 years ago by ▴ 10
3
votes
3
replies
542
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
2
replies
208
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
3
votes
2
replies
558
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
3
votes
4
replies
862
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
3
votes
1
reply
286
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 7 days ago by 41k • written 8 days ago by ▴ 40
50 results • Page 1 of 1
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Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient by JKim • 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Comment: Store output of matchPWM() by mat149 ▴ 70
out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) Error in do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) : '…
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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