Showing : geneexpression • reset
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
8 weeks ago jbgnielson • 0
2
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2
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388
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
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3
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1.5k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
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1
reply
459
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
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2
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1.7k
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FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
12 months ago CDSPARKS ▴ 10
0
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1
reply
611
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Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
0
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1
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2.3k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
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4
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1.6k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 19 months ago by 41k • written 19 months ago by • 0
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3
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973
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CountOverlap
GeneExpression ChIPSeqData
updated 19 months ago by 65k • written 19 months ago by ▴ 20
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433
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Free Gibbson energy RNA doublex
GeneExpression RNAinteract
20 months ago Tamina • 0
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0
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556
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
21 months ago hlee ▴ 10
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921
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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 21 months ago by ★ 1.3k • written 21 months ago by • 0
0
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1
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527
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Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
0
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1
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625
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 23 months ago by 65k • written 23 months ago by • 0
1
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1
reply
754
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Error while using champ.SVD function
GeneExpression
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
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1
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1.9k
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GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years ago by • 0
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0
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833
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Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.0 years ago by ★ 3.9k • written 2.0 years ago by • 0
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2
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810
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 2.1 years ago by • 0 • written 2.1 years ago by ▴ 10
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2
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2.0k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
2.5 years ago p.l.chen • 0
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2
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6.7k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.5 years ago by ★ 4.0k • written 2.6 years ago by ▴ 10
0
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2
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948
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Gene expression in R
limma edgeR Biobase GeneExpression
2.6 years ago sogol.bouyeh • 0
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2
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1.6k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
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18
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2.8k
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DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 2.9 years ago by 41k • written 3.0 years ago by • 0
1
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3
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955
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
1
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1
reply
725
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Accounting for fish body mass in DE?
GeneExpression edgeR
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
0
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1
reply
741
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.4 years ago by ▴ 490 • written 3.4 years ago by • 0
1
vote
3
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954
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Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
0
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0
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610
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.4 years ago coobzie • 0
2
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5
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11k
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Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 60
1
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4
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1.9k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 10
3
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1
reply
1.7k
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Processing several GSM from GEO database using Barcode and fRMA
frma barcode geneexpression gsm ncbi geo
updated 6.4 years ago by ▴ 830 • written 6.4 years ago by • 0
1
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4
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1.8k
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ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 6.7 years ago by ▴ 120 • written 6.8 years ago by ▴ 60
1
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3
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1.2k
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General suggestions regarding gene expression
geneexpression
updated 7.2 years ago by 50k • written 7.2 years ago by • 0
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0
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891
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Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
7.3 years ago shaheryar • 0
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0
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1.2k
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Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
7.7 years ago namilio • 0
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0
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1.1k
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Methylation and gene expression
methylation geneexpression
7.7 years ago Asma rabe ▴ 290
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2
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1.1k
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Methylation and gene expression data
methylation geneexpression
updated 7.9 years ago by ▴ 130 • written 7.9 years ago by ▴ 290
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3
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1.6k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 8.1 years ago by 65k • written 8.1 years ago by ▴ 20
1
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6
replies
1.8k
views
how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
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1
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1.3k
views
Error in MetaQC R package.
r metaqc microarray geneexpression
8.3 years ago Agaz Hussain Wani ▴ 260
0
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3
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1.8k
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problem with WGCNA
geneexpression
updated 8.4 years ago by ★ 3.0k • written 8.4 years ago by • 0
2
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5
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1.7k
views
heatmap in R
r language microarray geneexpression
updated 8.7 years ago by ★ 1.0k • written 8.7 years ago by • 0
1
vote
1
reply
1.2k
views
gene expression data analysis
microarray geneexpression
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
1
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1
reply
5.1k
views
NA p and p adjusted value
geneexpression
updated 8.7 years ago by ★ 3.0k • written 8.7 years ago by • 0
1
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2
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5.7k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
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3
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11k
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How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 8.8 years ago by ▴ 830 • written 8.8 years ago by ▴ 10
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0
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1.1k
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Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.4 years ago Peter.Wood • 0
3
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5
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8.5k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
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7
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9.2k
views
DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.5 years ago by ★ 13k • written 9.6 years ago by ▴ 10
4
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2
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4.0k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 9.6 years ago by 1.6k • written 9.6 years ago by ▴ 250
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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