Showing : RNASEQ • reset
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SVA method for estimating surrogate variables of RNA Seq
RNASeq sva svaseq
updated 3 days ago by 58k • written 3 days ago by • 0
2
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5
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164
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DESeq2 median of ratios normalization for signature score calculation
MRN RNASeq Normalization DESeq2
updated 8 days ago by 35k • written 10 days ago by • 0
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3
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144
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Transformations of the variance in RNA-seq count data DESeq2
RNASeq vst R rlog DESeq2
updated 7 days ago by 35k • written 11 days ago by • 0
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1
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84
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RNAseq using galaxy
RNASeq
updated 17 days ago by ▴ 970 • written 17 days ago by • 0
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69
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Complex design in DESeq2 doesn't seem to be supported in Glimma
limma Glimma RNASeq DESeq2
21 days ago Jonas • 0
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66
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Glimma: Error: Length of groups must be equal to the number of columns in counts
Glimma RNASeq
21 days ago Jonas • 0
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2
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151
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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter
batch RNASeq BatchEffect DESeq2
updated 18 days ago by 13k • written 22 days ago by • 0
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127
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gene id mapping issue
RNASeq
28 days ago waltsonwang88 • 0
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1
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123
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Outlier Removal WGCNA
RNASeq WGCNA
updated 20 days ago by 6.5k • written 29 days ago by • 0
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7
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313
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Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 4 weeks ago by 35k • written 4 weeks ago by • 0
3
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2
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183
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Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
5 weeks ago mohammedtoufiq91 ▴ 10
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1
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131
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RNA-Seq Workflow Vignette - library(airway) Missing "quants" directory
RNASeq DESeq2 airway
updated 5 weeks ago by 35k • written 5 weeks ago by • 0
2
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5
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331
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limma-trend and voom results do not agree
limma limma-trend voom RNASeq
9 weeks ago • updated 6 weeks ago Tyler Sagendorf • 0
1
vote
1
reply
161
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 7 weeks ago by 35k • written 7 weeks ago by • 0
1
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2
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197
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GEO RNASeq data query
GEOquery RNASeq GEO
updated 7 weeks ago by 21k • written 8 weeks ago by ▴ 10
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68
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Trouble with gene dendrogram
Network RNASeq WGCNA
7 weeks ago jms2520 • 0
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3
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345
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Problem getting soft threshold power using WGCNA for RNA-seq data
RNASeq WGCNA
8 weeks ago • updated 7 weeks ago jms2520 • 0
3
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1
reply
173
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Elastic Net for RNAseq data
Bioconductor RNASeq
updated 9 weeks ago by 35k • written 9 weeks ago by ▴ 10
1
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3
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209
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GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 9 weeks ago by 58k • written 9 weeks ago by ▴ 10
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1
reply
220
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Calculating gene expression dominance coefficient via DESeq2
RNASeq DESeq2
updated 9 weeks ago by 35k • written 9 weeks ago by • 0
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1
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120
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Summarising WGCNA data with modules and their corresponding gene ID and statistics
RNASeq WGCNA
9 weeks ago synat.keam • 0
1
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2
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197
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Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
10 weeks ago • updated 9 weeks ago Barista • 0
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95
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Gene expression changes in one condition
RNASeq Gene ExpressionData
10 weeks ago AZ ▴ 30
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104
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Proper normalization of batch effected corrected raw rsem rnaseq values for downstream unsupervised analyses
limma RNASeq rsem Normalization
10 weeks ago svlachavas ▴ 780
4
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4
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291
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FeatureCounts
counts subread RNASeq featurecounts
10 weeks ago Beth_b ▴ 20
1
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3
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185
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Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped RNAseq Rsamtools
10 weeks ago polemiraza ▴ 70
3
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3
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207
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Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 12 weeks ago by 58k • written 12 weeks ago by ▴ 10
2
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1
reply
204
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 12 weeks ago by 35k • written 3 months ago by • 0
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4
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233
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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
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5
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376
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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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248
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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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219
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How similar or disimilar are two sets of DEG?
DESeq2 RNASeq
updated 3 months ago by 35k • written 3 months ago by • 0
0
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2
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253
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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
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210
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Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 4 months ago by 58k • written 4 months ago by • 0
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3
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230
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4 months ago by 35k • written 4 months ago by • 0
0
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1
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257
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Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 4 months ago by 44k • written 4 months ago by • 0
0
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1
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167
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Job: Computational Biologist at Chinook Therapeutics
RNASeq Bioconductor Genomics
written 4 months ago by • 0
0
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2
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253
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log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
4 months ago Claire • 0
0
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4
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493
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Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 3.9 years ago by • 0
0
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1
reply
242
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featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 4 months ago by • 0 • written 4 months ago by • 0
1
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2
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218
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DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
4 months ago krawczyk.margarita • 0
0
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1
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257
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 4 months ago by ▴ 970 • written 5 months ago by • 0
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0
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103
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EventPointer on TCGA RNA-seq
RNASeq EventPointer
5 months ago Marie • 0
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3
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232
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 4 months ago by 35k • written 5 months ago by • 0
4
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4
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268
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Raw RNA-seq data: column names are sequences
RNASeq
updated 5 months ago by ▴ 970 • written 5 months ago by • 0
0
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1
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132
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PCA M3C
M3C RNASeq
updated 5 months ago by 3.4k • written 5 months ago by • 0
0
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2
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194
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Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
5 months ago peter.zhouyu • 0
0
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1
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213
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Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 5 months ago by ★ 27k • written 5 months ago by • 0
3
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1
reply
251
views
Compare two samples by Deseqs
DESeq2 RNASeq
updated 5 months ago by 3.4k • written 5 months ago by ▴ 10
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2
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228
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EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
5 months ago Ming ▴ 360
50 results • Page 1 of 1
Recent ...
Replies
Comment: Need help for ProStaR Stand-alone install by benoit.marchand • 0
Thank you for answering. I've just updated to Prostar v1.26.3 and confirm that the **Prostar()** command **now works** in R for me on linu…
Answer: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Votes
Comment: Need help for ProStaR Stand-alone install
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
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