Showing : DEseq • reset
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voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization graph limma convert edgeR DESeq Rsubread Normalization graph limma convert
updated 3 months ago by 47k • written 10.8 years ago by 6.5k
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821
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suggestions/comments on DESeq transcript wise analysis
convert DESeq convert DESeq
written 11.1 years ago by ▴ 190
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5
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676
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Potential outlier/high variance
deseq DESeq2
updated 11 months ago by 39k • written 11 months ago by • 0
2
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1
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595
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Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 10 months ago by ★ 1.2k • written 10 months ago by • 0
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5
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494
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Error in DEseq
DEseq RNASeqData
updated 9 months ago by ★ 2.5k • written 9 months ago by • 0
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2
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352
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DESeq2 is renaming gene names and lack of downregulated genes
DESeq DESeq2
8 months ago manwar • 0
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331
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Gene wise dispersion estimate Process - From the prior to the posterior
GLM prior DESeq LFC
updated 9 months ago by 39k • written 9 months ago by • 0
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4
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219
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Volcano plot becomes flipped when I add a third condition
DESeq2 volcanoplot deseq HELP contrast
updated 5 weeks ago by ▴ 700 • written 6 weeks ago by • 0
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1
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214
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How to design multifactor DESEQ2 formula?
DESEQ DESEQ2
updated 6 months ago by ★ 2.5k • written 6 months ago by • 0
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173
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What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 8 weeks ago by 39k • written 9 weeks ago by ▴ 10
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169
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 10 weeks ago by ★ 1.5k • written 10 weeks ago by • 0
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Comment: Help with Error in DiffBind by Rory Stark ★ 4.7k
Apologies. The first line should be result <- dba(sampleSheet=samples) I've gone back and edited previous replies to reflect this.
Answer: *** caught segfault *** , cause 'memory not mapped' by James W. MacDonald 62k
You are unfortunately running out of RAM. As you note, you could possibly use `frma`, after generating frozen vectors using the `frmaTools`…
Comment: Help with Error in DiffBind by Chris • 0
Thanks Rory! result <- dba(samples) Error in if ((length(callers) == 1) & (callers[1] == "counts")) { : argument is of len…
Answer: Help with Error in DiffBind by Rory Stark ★ 4.7k
In your case, with only two replicates in each sample group, you can not perform a default analysis using only `dba.analyze()`. I suggest t…
Comment: Help with Error in DiffBind by Rory Stark ★ 4.7k
Looks like you should either delete the file > /labs/PI/atacseq_output_03172023/bwa/merged_library/DISEASED_REP2.mLb.clN.sorted.bam.bai …
Votes
Comment: Help with Error in DiffBind
WGCNA: Module preservation vs consensus analysis
WGCNA: Module preservation vs consensus analysis
Answer: Help with Error in DiffBind
Comment: Help with Error in DiffBind
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