Showing : RNA seq • reset
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How to create manhattan plot with DESeq2
deseq2 mahattan plot RNA Seq
updated 5.3 years ago by ▴ 150 • written 6.3 years ago by • 0
2
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5
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5.4k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
updated 5.8 years ago by ★ 13k • written 5.8 years ago by ▴ 840
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3
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1.6k
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Normalization of RNA seq data
RNA seq cpm
updated 5.8 years ago by ★ 4.0k • written 5.8 years ago by • 0
4
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4
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1.6k
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Custom gene annotations for SGSeq
sgseq alternative splicing rna seq
updated 18 months ago by • 0 • written 6.2 years ago by • 0
1
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4
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1.4k
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Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger RNA Seq
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 30
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853
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searching for specific RNA sequences
rna seq
6.2 years ago adeler001 • 0
0
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2
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1.4k
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using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq SGSeq Alternative splicing
updated 6.3 years ago by ▴ 260 • written 6.3 years ago by • 0
0
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1
reply
876
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51 views DESeq2 RNAseq differential expression analysis
deseq2 likelihood ratio rna seq wald test
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
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2
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1.6k
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Need help cprrecting overlappinge genes on valcano plot
volcano plot rna seq
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
1
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5
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2.0k
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Time course experiment using limma with voom
limma voom RNA Seq Time-course experiments
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
5
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3
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1.8k
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Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq wgcna
updated 6.7 years ago by ★ 3.0k • written 6.7 years ago by ▴ 20
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2
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2.8k
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adapter trimming paired vs unpaired reads
rna seq trimmomatic trimming adapter trimming paired analysis
6.7 years ago Mozart ▴ 30
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2.3k
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Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
8.0 years ago lawarde.ankita1 ▴ 30
13 results • Page 1 of 1
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Answer: lfc shrinkage estimator in DESeq2 by plumsgorillas • 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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