Showing : RnaSeq • reset
25
votes
37
replies
12k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 8.0 years ago by 52k • written 8.0 years ago by ▴ 840
0
votes
28
replies
3.8k
views
Job: Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq data integration single-cell pacbio across species Job
6.8 years ago bgee • 0
2
votes
23
replies
4.2k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
52
votes
20
replies
48k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 8.6 years ago by • 0 • written 9.1 years ago by ▴ 110
1
vote
19
replies
28k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 10
2
votes
18
replies
3.9k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
6.8 years ago stephan.emmrich ▴ 10
0
votes
18
replies
6.8k
views
WGCNA error in network construction ?
microarray rnaseq
7.8 years ago m.azhar ▴ 10
7
votes
18
replies
4.1k
views
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
rnaseq edger differential gene expression
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by • 0
0
votes
17
replies
3.1k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ▴ 330
18
votes
17
replies
4.8k
views
How to model a comparison between comparisons in edgeR?
edger rnaseq
updated 9.9 years ago by ★ 7.9k • written 9.9 years ago by ▴ 60
2
votes
17
replies
3.0k
views
Computationally Singular Matrices - DESeq
deseq2 rnaseq sva
updated 2.2 years ago by 43k • written 5.8 years ago by • 0
3
votes
16
replies
2.8k
views
Atena package - error (new user)
RNAseq R Atena
2.3 years ago • updated 23 months ago lalanis1 • 0
4
votes
16
replies
8.2k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 10 months ago by • 0 • written 9.7 years ago by ▴ 160
32
votes
16
replies
19k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 6.7 years ago by ▴ 20 • written 8.5 years ago by ▴ 200
4
votes
15
replies
4.8k
views
DESeq2 for mulitple tissues under 2 conditions and contrast options
deseq2 rnaseq featurecounts DESeqDataSetFromMatrix
updated 7.1 years ago by 43k • written 7.2 years ago by ▴ 10
3
votes
15
replies
3.7k
views
How to ellipse a subset of data PCA biplot?
biplot PCA RNASeq PCAtools
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by ▴ 10
7
votes
15
replies
5.7k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 6.6 years ago by 52k • written 6.6 years ago by ▴ 60
5
votes
15
replies
5.9k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 19 months ago by 67k • written 7.5 years ago by ▴ 10
0
votes
14
replies
2.9k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
3.5 years ago Abhishek • 0
0
votes
14
replies
4.8k
views
Using name parameter in DESeq2-results function
deseq2 rnaseq
7.2 years ago muratcokol • 0
17
votes
14
replies
47k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.6 years ago by • 0 • written 7.5 years ago by ▴ 20
2
votes
14
replies
2.4k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 30
4
votes
14
replies
1.8k
views
Application of quantro to RNASeq: I do not get the same results as are in the quantro paper supplement
quantro RNASeq
updated 4.6 years ago by ▴ 80 • written 4.7 years ago by ▴ 30
11
votes
14
replies
4.5k
views
Setting up the Design Matrix
rnaseq edgeR multiple factor design design matrix
9.0 years ago Yogender Gowtham ▴ 20
6
votes
14
replies
2.5k
views
Help analyzing RNA-seq data from FPKM values with multiple time points
rnaseq limma
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
6
votes
14
replies
6.5k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.0 years ago by 52k • written 10.1 years ago by • 0
4
votes
14
replies
9.4k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
9.5 years ago nickp60 • 0
21
votes
13
replies
16k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger rnaseq
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 50
22
votes
13
replies
28k
views
gene dispersion, what does it mean?
gener rnaseq
updated 22 months ago by 52k • written 9.1 years ago by ▴ 80
12
votes
13
replies
8.5k
views
EdgeR Differential Expression analysis with NAs
EdgeR rnaseq NA
updated 10.3 years ago by ★ 28k • written 10.3 years ago by • 0
1
vote
13
replies
4.7k
views
Similar to Tukey Post hoc after ANOVA
rnaseq multiple comparisons post hoc deseq2
8.6 years ago • updated 7.9 years ago laianavarromartin ▴ 20
1
vote
13
replies
15k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
8.4 years ago yjliu1127 • 0
3
votes
13
replies
4.9k
views
RPKM and FPKM
rnaseq
9.5 years ago Asma rabe ▴ 290
0
votes
13
replies
4.5k
views
DESeq2: collapseReplicates error
deseq2 rnaseq differential gene expression
8.4 years ago ta_awwad ▴ 10
3
votes
12
replies
5.3k
views
The calculation of regularized logarithm
rnaseq deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
3
votes
12
replies
2.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
3
votes
12
replies
4.3k
views
Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga rnaseq glmnet voom deseq2
7.9 years ago • updated 7.8 years ago panagiotis.mokos ▴ 40
0
votes
12
replies
2.6k
views
RNAseq machine learning classifier
RNASeq Microarray RNASeq Microarray
updated 11.5 years ago by ▴ 60 • written 11.5 years ago by ▴ 370
5
votes
12
replies
8.2k
views
Remove batch effect in small RNASeq study (SVA or others?)
RNASeq Alignment edgeR sva
updated 10.0 years ago by 52k • written 10.7 years ago by ★ 1.0k
1
vote
12
replies
5.2k
views
EdgeR: replicated pools, yes or not?
RNASeq Microarray edgeR RNASeq Microarray edgeR
updated 10.7 years ago by ★ 7.9k • written 10.7 years ago by ★ 13k
6
votes
12
replies
19k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
0
votes
12
replies
2.1k
views
DESeq2 different versions
rnaseq r deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
12
votes
12
replies
2.6k
views
FDR does not change between genes in edgeR
RNAseq edgeR
updated 6.0 years ago by 52k • written 6.0 years ago by ▴ 30
5
votes
12
replies
2.5k
views
DESeq2 multi-factor comparison problem
deseq2 rnaseq
9.7 years ago Vivek.b ▴ 100
4
votes
12
replies
5.3k
views
remove batch effect using limma
limma rnaseq batch effect pearsoncorrelation
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
1
vote
12
replies
2.3k
views
How to find the differentially expressed genes for paired tumor normal samples without any biological replicates?
rnaseq deseq2
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
7
votes
12
replies
4.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 15 months ago by • 0 • written 3.9 years ago by • 0
6
votes
11
replies
4.3k
views
edgeR on extremely large dataset
edgeR rnaseq
9.1 years ago martiningi ▴ 40
1
vote
11
replies
7.8k
views
RNA Seq data analysis using Salmon and tximport
RNAseq tximport
7.3 years ago tanyabioinfo ▴ 20
3
votes
11
replies
4.0k
views
DESeq function taking too long
deseq2 deseq factor rnaseq
updated 7.5 years ago by ★ 3.0k • written 7.5 years ago by ▴ 30
50 results • Page 1 of 1
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Replies
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
Votes
Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
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