Showing : differential gene expression • reset
0
votes
1
reply
903
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 4 months ago by ★ 4.0k • written 6.0 years ago by • 0
1
vote
9
replies
5.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 6.1 years ago by • 0
5
votes
14
replies
4.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 24 months ago by ★ 4.0k • written 5.8 years ago by ▴ 60
1
vote
3
replies
809
views
Favorite plotting tweak for padj=0
deseq2 differential gene expression
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Error loading sample and control data using Ballgown due to different i_id in i_data.ctab
ballgown i_data.ctab differential gene expression
updated 3.6 years ago by ▴ 210 • written 3.6 years ago by • 0
2
votes
3
replies
981
views
Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq differential gene expression
3.7 years ago DataFanatic ▴ 10
0
votes
1
reply
910
views
Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 4.0 years ago by ★ 28k • written 4.1 years ago by • 0
8
votes
7
replies
1.9k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 4.9 years ago by • 0 • written 5.6 years ago by ▴ 20
0
votes
0
replies
863
views
I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
limma microarray differential gene expression linear regression edger
5.2 years ago ravelarvargas • 0
1
vote
4
replies
1.2k
views
I am having trouble recreating the linear regression results published in an Alzheimer's paper
limma edger linear regression microarray differential gene expression
5.2 years ago ravelarvargas • 0
3
votes
5
replies
7.6k
views
How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 5.2 years ago by ★ 1.3k • written 5.2 years ago by • 0
1
vote
5
replies
1.2k
views
My linear regression model is giving me too many differentially expressed genes
limma rna-seq differential gene expression edger linear regression
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
5
votes
3
replies
1.4k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
5.3 years ago S.Webb6 ▴ 40
2
votes
8
replies
3.8k
views
MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 5.3 years ago by 50k • written 5.3 years ago by • 0
1
vote
3
replies
1.3k
views
how to find expressed genes in RNAseq
deseq2 rnaseq differential gene expression featurecounts rnaseqGene
5.4 years ago • updated 5.3 years ago melkile26 • 0
0
votes
5
replies
1.3k
views
NanoStringDiff analysis with confounding factors
differential gene expression nanostring confounding factors
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
3
votes
6
replies
2.2k
views
Controlling numerical covariates: differential gene expression with limma voom
limma voom differential gene expression rnaseq R
updated 5.4 years ago by ▴ 270 • written 5.4 years ago by • 0
0
votes
2
replies
4.4k
views
DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 5.4 years ago by • 0 • written 5.4 years ago by • 0
0
votes
1
reply
1.0k
views
DESeq2 - shrunken log fold changes and threshold test
deseq2 lfcshrink lfcthreshold differential gene expression
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
0
votes
0
replies
1.1k
views
Error while loading the data structrure in the ballgown tool
ballgown rnaseq differential gene expression new tuxedo pipleine
5.5 years ago Mithil Gaikwad • 0
2
votes
3
replies
1.5k
views
Using LIMMA for differential gene analysis of microarray data
limma differential gene expression ncbi geo affymetrix microarrays
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
0
votes
7
replies
1.9k
views
DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression
5.5 years ago bharata1803 ▴ 60
3
votes
3
replies
1.2k
views
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 830
2
votes
3
replies
1.4k
views
Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
9
votes
5
replies
4.2k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 5.5 years ago by ★ 13k • written 5.5 years ago by • 0
0
votes
1
reply
768
views
Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
1
vote
2
replies
1.1k
views
DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression
updated 5.5 years ago by 41k • written 5.5 years ago by ▴ 20
5
votes
6
replies
1.5k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
2
replies
1.2k
views
deseq2 analysis multiple factor and 4 different time points
edger and deseq2 differential gene expression bias
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by • 0
2
votes
7
replies
2.6k
views
How to block for a subject in a 2 factor design formula
deseq2 differential gene expression rnaseq
5.6 years ago Onyi Ukay • 0
1
vote
1
reply
2.0k
views
EdgeR between unequal group sizes?
edger differential gene expression rnaseq
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 30
4
votes
4
replies
1.1k
views
EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
2
votes
4
replies
2.1k
views
EdgeR analysis batch effect
edger differential gene expression
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
0
votes
1
reply
1.5k
views
Combining biological replicates from raw counts for use in differential gene expression/normalization (DESeq2 and edgeR)
differential gene expression biologicalreplicates raw_counts
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
1
vote
7
replies
1.1k
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 5.6 years ago by 50k • written 5.6 years ago by • 0
0
votes
0
replies
857
views
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
edge differential gene expression timecourse interaction
5.7 years ago rubi ▴ 110
1
vote
7
replies
1.7k
views
skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers
updated 5.7 years ago by ★ 7.9k • written 5.7 years ago by ▴ 20
0
votes
4
replies
1.7k
views
Simple differential expression analysis for 2 groups
differential gene expression agilent microarrays microarray DEA Limma
5.7 years ago christiangriffioen • 0
1
vote
6
replies
2.0k
views
Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
3
votes
8
replies
2.7k
views
EdgeR for differential analysis between two cell lines without replication
edger differential gene expression rnaseq
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 110
0
votes
2
replies
2.2k
views
What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 80
1
vote
5
replies
1.1k
views
Differential analysis based on selection of random samples
r differential gene expression deseq2 bioconductor rnaseq
updated 5.8 years ago by 41k • written 5.8 years ago by ▴ 60
1
vote
1
reply
832
views
DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
1
vote
0
replies
1.2k
views
covariate vs adjustvars
ballgown rnaseq differential gene expression tuxedo
5.8 years ago justinjj ▴ 10
1
vote
1
reply
764
views
PROBLEM WHILE IMPORTING FOR edgeR
differential gene expression edger
5.8 years ago prakashpandey1111 • 0
2
votes
1
reply
855
views
Differential analysis between 2 groups (n=1) vs (n=3) moderated t-test
moderated t-test limma differential gene expression small sample size
updated 5.8 years ago by 50k • written 5.8 years ago by • 0
1
vote
1
reply
1.7k
views
non-integer counts in DESeq2
deseq2 differential gene expression
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
0
votes
2
replies
1.6k
views
Removing batch effect from gene expression before Limma linear modelling
Limma differential gene expression batch effect correction covariates
updated 5.9 years ago by 50k • written 5.9 years ago by • 0
0
votes
0
replies
1.2k
views
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
5.9 years ago manuelmendoza • 0
7
votes
6
replies
5.7k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards • All
Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
France, 2 minutes ago
China, 1 hour ago
India, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
EMBL Heidelberg, 2 hours ago
Traffic: 572 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6