Showing : RnaSeq • reset
2
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2
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2.0k
views
Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 60
0
votes
4
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1.2k
views
limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq limma
3.7 years ago danphillips28 ▴ 10
0
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1
reply
2.3k
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GSEA using custom GO annotations
RNASeq GSEA
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by ▴ 10
0
votes
1
reply
2.8k
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
4
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1
reply
3.7k
views
Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
1
vote
1
reply
1.0k
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 40
4
votes
6
replies
13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.7 years ago treebig44 ▴ 40
0
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0
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1.2k
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
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2
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1.8k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
3.7 years ago tcalvo ▴ 100
0
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2
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946
views
Differential expression in fixed windows
DESeq2 RNASeq
3.7 years ago anatmela • 0
2
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1
reply
1.2k
views
DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
votes
1
reply
1.3k
views
Controlling for sex variance in Galaxy DESeq2
DESeq2 RNASeq Galaxy
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
1
reply
2.3k
views
95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2 RNASeq
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by • 0
0
votes
1
reply
1.9k
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
votes
4
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2.3k
views
How do you get averages of each group in Limma output
RNASeq limma
3.8 years ago Matthew • 0
0
votes
6
replies
5.4k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 60
0
votes
4
replies
1.8k
views
Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 3.8 years ago by ★ 1.4k • written 3.8 years ago by • 0
0
votes
3
replies
3.4k
views
DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
0
votes
3
replies
2.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.8 years ago by 53k • written 3.8 years ago by ▴ 90
1
vote
3
replies
2.1k
views
Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 2.8 years ago by • 0 • written 3.8 years ago by • 0
0
votes
2
replies
1.4k
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.8 years ago IamFrofro • 0
0
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0
replies
845
views
RNA seq of 4 groups p_values
R analysis p_values RNASeq
updated 3.8 years ago by 21k • written 3.8 years ago by • 0
0
votes
0
replies
1.5k
views
SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
3
votes
5
replies
4.7k
views
DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 3.8 years ago by 43k • written 3.9 years ago by ▴ 10
1
vote
3
replies
2.3k
views
Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 3.8 years ago by 43k • written 3.9 years ago by • 0
0
votes
1
reply
1.5k
views
RNAseq using galaxy
RNASeq
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by • 0
0
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0
replies
829
views
Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
3.9 years ago Jonas • 0
0
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0
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1.5k
views
Glimma: Error: Length of groups must be equal to the number of columns in counts
Glimma RNASeq
3.9 years ago Jonas • 0
0
votes
2
replies
1.5k
views
Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 3.9 years ago by ★ 13k • written 3.9 years ago by • 0
0
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0
replies
1.5k
views
gene id mapping issue
RNASeq
3.9 years ago waltsonwang88 • 0
0
votes
1
reply
1.5k
views
Outlier Removal WGCNA
RNASeq WGCNA
updated 3.9 years ago by 6.7k • written 3.9 years ago by ▴ 10
2
votes
9
replies
6.2k
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 3.5 years ago by 43k • written 3.9 years ago by ▴ 10
4
votes
4
replies
3.5k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 23 months ago by 53k • written 3.9 years ago by ▴ 10
0
votes
1
reply
996
views
RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
3
votes
5
replies
3.7k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
4.0 years ago • updated 3.9 years ago Tyler Sagendorf ▴ 10
1
vote
1
reply
1.2k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
vote
2
replies
3.6k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.9 years ago by • 0 • written 4.0 years ago by ▴ 10
0
votes
3
replies
2.4k
views
Problem getting soft threshold power using WGCNA for RNA-seq data
RNASeq WGCNA
4.0 years ago jms2520 ▴ 10
4
votes
1
reply
2.0k
views
Elastic Net for RNAseq data
Bioconductor RNASeq
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 20
2
votes
3
replies
2.6k
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 20
0
votes
1
reply
1.6k
views
Calculating gene expression dominance coefficient via DESeq2
RNASeq DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
1
reply
1.7k
views
Summarising WGCNA data with modules and their corresponding gene ID and statistics
RNASeq WGCNA
4.0 years ago synat.keam • 0
1
vote
2
replies
1.6k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
4.0 years ago Barista • 0
0
votes
0
replies
814
views
Gene expression changes in one condition
RNASeq Gene ExpressionData
4.0 years ago AZ ▴ 30
0
votes
0
replies
1.0k
views
Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
4.0 years ago svlachavas ▴ 840
4
votes
4
replies
6.7k
views
FeatureCounts
counts subread RNASeq featurecounts
4.0 years ago k___ ▴ 30
1
vote
3
replies
2.7k
views
Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped RNAseq Rsamtools
4.0 years ago polemiraza ▴ 70
3
votes
3
replies
1.0k
views
Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 20
4
votes
1
reply
3.1k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
1,409 results • Page 6 of 29
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Comment: Alternative to BrainArray custom CDF packages for Affymetrix chips? by insuraasanaa3scetaxrealty • 0
Lamento que el acceso a los paquetes BrainArray esté fallando; cuando ocurren estos problemas, es util contar con recursos alternativos bie…
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
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Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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