Showing : EdgeR • reset
3
votes
2
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1.5k
views
How to calculate average log2 CPM with batch effect?
edger limma cpm
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 370
6
votes
5
replies
3.4k
views
edgeR compilation error: with g++ 4.9.2 and R-5.0 on linux platform
edger compilation error
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 60
2
votes
1
reply
965
views
edgeR with related individuals?
edgeR related design matrix
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
3
votes
3
replies
1.5k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 10
1
vote
1
reply
2.5k
views
EdgeR between unequal group sizes?
edger differential gene expression rnaseq
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 30
1
vote
9
replies
3.5k
views
EDASeq, RUVSeq and edgeR together
edaseq ruvseq edgeR
updated 7.1 years ago by ▴ 980 • written 7.1 years ago by ▴ 10
1
vote
3
replies
4.8k
views
the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
edger limma logfc
updated 2.7 years ago by 53k • written 7.1 years ago by • 0
2
votes
4
replies
2.7k
views
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
deseq2 edger fpkm counts fc
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
1
vote
2
replies
1.6k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2 edger fpkm counts TCGA
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
3
votes
3
replies
1.3k
views
use only lib size as normalizing factor in edgeR
edger
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 30
2
votes
2
replies
1.2k
views
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
1
vote
5
replies
1.1k
views
can i only analyse some genes different RNAseq expression analyse not the whole transcriptome RNAseq analyse by DESeq2 or edgeR
deseq2 edger
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
2
votes
8
replies
2.7k
views
edgeR: design matrix for methylation analysis
edger methylation
updated 7.1 years ago by 53k • written 7.3 years ago by • 0
1
vote
2
replies
2.9k
views
why the p value and FDR is different between classic exactTest and glm glmQLFTest in edgeR?
edger
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
4
votes
4
replies
1.6k
views
EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
2
votes
4
replies
2.8k
views
EdgeR analysis batch effect
edger differential gene expression
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
7
votes
2
replies
2.0k
views
Pre-ranked camera gene set testing with edgeR results
limma camera cameraPR edgeR gene set testing
updated 7.1 years ago by 53k • written 7.1 years ago by ▴ 60
1
vote
7
replies
1.8k
views
How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
edgeR R differential gene expression up-regulation gene list
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
3
votes
4
replies
1.9k
views
edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger rnaseq gene expression bioinformatics
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
0
votes
2
replies
1.7k
views
RNA-seq unbalanced batch effect correction
rnaseq edger batch effect
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
3
votes
1
reply
1.6k
views
DE genes comparison of different treatments from microarray and RNAseq data
microarray deseq2 limma edgeR
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
4
votes
3
replies
1.5k
views
CNV-expression testing with edgeR
edgeR
7.2 years ago • updated 7.1 years ago Ludwig Geistlinger ▴ 70
1
vote
4
replies
3.8k
views
EdgeR filtering, gene expression, cpm cutoff
edger Tutorial
updated 7.2 years ago by ▴ 400 • written 7.2 years ago by • 0
3
votes
16
replies
3.9k
views
Error in glmFit.default() : y is not a numeric matrix
edger
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 20
3
votes
1
reply
970
views
Can limma/other DE algorithms be used for differential analysis of chemical descriptors?
limma edger deseq2 cheminformatics
updated 7.2 years ago by ★ 29k • written 7.2 years ago by • 0
4
votes
6
replies
4.3k
views
EdgeR normalization factors - do they take into account library size?
edgeR
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 60
2
votes
4
replies
3.0k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 3 months ago by • 0 • written 7.2 years ago by • 0
2
votes
2
replies
1.7k
views
Change legend names when using plotBCV
edger plot Tutorial
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
2
votes
2
replies
669
views
EdgeR Multivariate Analysis question
edger limma
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
0
votes
1
reply
1.0k
views
Installation of package 'FDb.InfiniumMethylation.hg19' fails
bioconductor fdb.infiniummethylation.hg19 edger
7.2 years ago m.nabais • 0
0
votes
4
replies
2.2k
views
Error in RnaSeqGeneEdgeRQL
dgelist edger RnaSeqGeneEdgeRQL
updated 7.2 years ago by 53k • written 7.2 years ago by • 0
0
votes
1
reply
2.0k
views
Is there a way to specify the pathway level of classification that we want in kegga function from edgeR?
edgeR kegga KEGG
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
3
replies
1.4k
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 7.2 years ago by ★ 29k • written 7.2 years ago by • 0
2
votes
5
replies
5.4k
views
Batch Effect Correction
batch effect removebatcheffect edgeR rld DEseq2
7.2 years ago Antonio Ahn ▴ 10
3
votes
4
replies
1.8k
views
Cannot retrieve DE genes from goana GO terms
limma goana edger
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 370
4
votes
2
replies
1.0k
views
edgeR coefficients for DEG analysis
edgeR
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 10
0
votes
8
replies
2.1k
views
weights must be finite positive value
edger estimatedispersions
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
ProcessAmplicons using very little memory on big job?
edgeR processamplicons memory problem
7.3 years ago sdalin • 0
2
votes
4
replies
1.9k
views
Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
edger cpm non-specific filtering rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 840
3
votes
8
replies
3.2k
views
EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 120
2
votes
3
replies
965
views
Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
rnaseq limma edger
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 60
4
votes
3
replies
1.6k
views
Differential profile for only one normal - tumor pair
edger degs paired design
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 10
5
votes
1
reply
1.4k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
1
vote
1
reply
1.0k
views
PROBLEM WHILE IMPORTING FOR edgeR
differential gene expression edger
7.3 years ago prakashpandey1111 • 0
0
votes
6
replies
1.3k
views
Identify the normalized count from differential expression
edger
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
2
votes
1
reply
1.1k
views
Batch Variation-MDS Plot
edger R batch effect
updated 7.3 years ago by 53k • written 7.3 years ago by • 0
0
votes
2
replies
1.3k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 90
0
votes
6
replies
2.1k
views
unexpected p-value histogram in edgeR
edgeR p-value distribution
updated 7.3 years ago by ★ 7.9k • written 7.3 years ago by • 0
3
votes
2
replies
2.1k
views
edgeR: problem with the quasi-likelihood F-test
edgeR glmQLFTest
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 10
1
vote
4
replies
1.6k
views
edgeR - how to build design for matched case-control study with repeated measurement
edger
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
2,031 results • Page 15 of 41
Recent ...
Replies
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by Gabriel • 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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