Showing : RNASeqData • reset
2
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DESeq2: how to integrate a manually edited matrix into full argument of DESeq
RNASeqData DESeq2
22 days ago • updated 17 days ago khaveh ▴ 10
0
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2
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122
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Combining HTSeq and RNA-SeQ for differential analysis
RNASeqData
6 weeks ago szomolay • 0
0
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1
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136
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Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 3 months ago by ▴ 650 • written 3 months ago by • 0
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3
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180
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 3 months ago by ▴ 840 • written 3 months ago by • 0
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1
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134
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t.fit stops in masigpro while running RNA seq data
RNASeqData maSigPro
4 months ago subashika • 0
3
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2
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451
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handling outliers with DESeq2
RNASeqData DESeq2 Outliers
4 months ago paty ▴ 20
1
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3
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297
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Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
4 months ago dantasezequiel1 • 0
1
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15
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500
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between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
5 months ago demisa • 0
0
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6
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281
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while doing co-expression network analysis, I am getting an error
RNASeqData
5 months ago Rishav ▴ 20
2
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8
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358
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While trying to remove non differentially expressed genes through limma, I am getting a warning
RNASeqData
updated 5 months ago by 43k • written 5 months ago by ▴ 20
3
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4
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316
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GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
5 months ago hgalmoore • 0
0
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4
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495
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How to use combat in order to remove batch effects?
BatchEffect DESeq2 RNASeqData
written 6 months ago by • 0
3
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2
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254
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
6 months ago Wuschel ▴ 10
1
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6
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300
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Contamination in bulkseq samples. Looking at correlated genes?
RNASeqData DESeq2 rnaseqGene
7 months ago Seaweed • 0
7
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5
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448
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Normalise to a housekeeping gene in DESEq2
DESeq2 housekeeping R RNASeqData
9 months ago ecg1g15 • 0
3
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6
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441
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 9 months ago by 34k • written 9 months ago by ▴ 20
2
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4
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516
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Compare 3 RNASeq groups with no control in DESeq2
anova RNASeqData tukeyTest DESeq2
9 months ago ecg1g15 • 0
0
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1
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165
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RNA gene expression data retrieval for breast cancer subtypes
RNASeqData GenomeInfoDb
updated 9 months ago by 3.4k • written 9 months ago by • 0
0
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3
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1.4k
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Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 10 months ago by 58k • written 10 months ago by • 0
0
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1
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763
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RNASeq analysis - Test for effect of two variables on one (Genotype)
deseq2 multiple factor design rnaseqdata
updated 5.4 years ago by 34k • written 5.4 years ago by ▴ 70
1
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2
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1.0k
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Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 6.6 years ago by ★ 1.9k • written 6.6 years ago by ▴ 150
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10
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1.8k
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GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 7.2 years ago by ▴ 320 • written 7.2 years ago by ★ 6.7k
22 results • Page 1 of 1
Recent ...
Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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