Showing : rnaseq • reset
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Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 6 hours ago by ▴ 970 • written 12 hours ago by • 0
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3
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100
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DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 1 day ago by ▴ 160 • written 2 days ago by • 0
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3
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98
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using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 2 days ago by 44k • written 3 days ago by ▴ 70
1
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2
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65
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 3 days ago by 35k • written 3 days ago by • 0
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2
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69
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Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3 days ago IamFrofro • 0
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0
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46
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RNA seq of 4 groups p_values
R analysis p_values RNASeq
updated 5 days ago by 21k • written 6 days ago by • 0
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0
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47
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SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 10 days ago by 58k • written 10 days ago by • 0
2
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5
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180
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DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 15 days ago by 35k • written 17 days ago by • 0
1
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3
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151
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Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 14 days ago by 35k • written 18 days ago by • 0
0
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1
reply
88
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RNAseq using galaxy
RNASeq
updated 24 days ago by ▴ 990 • written 25 days ago by • 0
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0
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75
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
28 days ago Jonas • 0
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0
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72
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Glimma: Error: Length of groups must be equal to the number of columns in counts
Glimma RNASeq
29 days ago Jonas • 0
0
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2
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167
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 25 days ago by 13k • written 29 days ago by • 0
0
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0
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133
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gene id mapping issue
RNASeq
5 weeks ago waltsonwang88 • 0
0
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1
reply
131
views
Outlier Removal WGCNA
RNASeq WGCNA
updated 27 days ago by 6.6k • written 5 weeks ago by • 0
0
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7
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333
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Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
3
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2
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190
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
6 weeks ago mohammedtoufiq91 ▴ 10
0
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1
reply
139
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RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 6 weeks ago by 35k • written 6 weeks ago by • 0
2
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5
replies
344
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
10 weeks ago • updated 7 weeks ago Tyler Sagendorf • 0
1
vote
1
reply
166
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 8 weeks ago by 35k • written 8 weeks ago by • 0
1
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2
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216
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GEO RNASeq data query
GEOquery RNASeq GEO
updated 8 weeks ago by 21k • written 9 weeks ago by ▴ 10
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0
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77
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Trouble with gene dendrogram
Network RNASeq WGCNA
8 weeks ago jms2520 • 0
0
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3
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353
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Problem getting soft threshold power using WGCNA for RNA-seq data
RNASeq WGCNA
9 weeks ago • updated 8 weeks ago jms2520 • 0
3
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1
reply
182
views
Elastic Net for RNAseq data
Bioconductor RNASeq
updated 10 weeks ago by 35k • written 10 weeks ago by ▴ 10
1
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3
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231
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GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 10 weeks ago by 58k • written 10 weeks ago by ▴ 10
0
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1
reply
223
views
Calculating gene expression dominance coefficient via DESeq2
RNASeq DESeq2
updated 10 weeks ago by 35k • written 10 weeks ago by • 0
0
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1
reply
129
views
Summarising WGCNA data with modules and their corresponding gene ID and statistics
RNASeq WGCNA
10 weeks ago synat.keam • 0
1
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2
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211
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Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
11 weeks ago Barista • 0
0
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0
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103
views
Gene expression changes in one condition
RNASeq Gene ExpressionData
11 weeks ago AZ ▴ 30
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0
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107
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Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
11 weeks ago svlachavas ▴ 780
4
votes
4
replies
304
views
FeatureCounts
counts subread RNASeq featurecounts
11 weeks ago Beth_b ▴ 20
1
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3
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190
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Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped RNAseq Rsamtools
11 weeks ago polemiraza ▴ 70
3
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3
replies
213
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Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 3 months ago by 58k • written 3 months ago by ▴ 10
2
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1
reply
212
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 3 months ago by 35k • written 3 months ago by • 0
0
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4
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236
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How to analyze 10 samples (5 control, 5 treatment) which perform the experiment from different day
DESeq2 RNASeq
3 months ago Yosapol • 0
0
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5
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382
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RNA-seq with patient samples without replicates with multiple timepoints
edgeR RNASeq multi
updated 3 months ago by 44k • written 3 months ago by • 0
0
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2
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256
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How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 3 months ago by 44k • written 3 months ago by • 0
0
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2
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224
views
How similar or disimilar are two sets of DEG?
DESeq2 RNASeq
updated 4 months ago by 35k • written 4 months ago by • 0
0
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2
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266
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 4 months ago by 44k • written 4 months ago by • 0
0
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1
reply
221
views
Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 4 months ago by 58k • written 4 months ago by • 0
0
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3
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237
views
DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4 months ago by 35k • written 5 months ago by • 0
0
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1
reply
261
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 5 months ago by 44k • written 5 months ago by • 0
0
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1
reply
170
views
Job: Computational Biologist at Chinook Therapeutics
RNASeq Bioconductor Genomics
written 5 months ago by • 0
0
votes
2
replies
261
views
log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
5 months ago Claire • 0
0
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4
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500
views
Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 3.9 years ago by • 0
0
votes
1
reply
266
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 5 months ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
223
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
5 months ago krawczyk.margarita • 0
0
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1
reply
274
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 5 months ago by ▴ 990 • written 5 months ago by • 0
0
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0
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108
views
EventPointer on TCGA RNA-seq
RNASeq EventPointer
5 months ago Marie • 0
0
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3
replies
235
views
DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 4 months ago by 35k • written 5 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
You can have as many columns as you like in coldata, only those specified in the design will be used when you do the DESeq command So sur…
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Matthew • 0
Thanks for the suggestion, I'll give that a try! Based on the PCA, all three factors do tend to influence the results, so I'll try the colu…
Comment: fgsea not downloading due to new r version. Is there a way around this? by amir.khan • 0
Seems to have done the trick and worked. thanks!
Comment: Multi-factor paired RNAseq differential analysis with DEseq2 by Michael Love 35k
Just to underscore swbarnes2 advice above, I'd also recommend discussing statistical design with a local statistician or someone familiar w…
Answer: Multi-factor paired RNAseq differential analysis with DEseq2 by swbarnes2 ▴ 970
First, I'd start by looking at all your samples in PCA. Does sex have a strong effect? Does it make sense to compare one tissue with anot…
Votes
Answer: fgsea not downloading due to new r version. Is there a way around this?
Comment: Unable to install Rhtslib in R-4.1.1
Answer: fgsea not downloading due to new r version. Is there a way around this?
Answer: Swish with more than two conditions. Add support for contrasts?
Answer: ERROR: unable to find an inherited method for function ‘dispersions<-’ for signa
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