Showing : RNAseq analysis • reset
0
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edgeR: "no non-missing arguments to min; returning Inf" after filterByExpression
filterByExpression edgeR RNAseq analysis edger
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
0
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4
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809
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RNA seq data
rnaseq analysis
updated 6.0 years ago by 67k • written 6.0 years ago by • 0
6
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14
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3.4k
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Robust transformation of raw RNA-seq counts for exploratory data analysis and hierarchical clustering
rnaseq analysis variancestabilizingtransformation normalization cpm edger
updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 840
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2
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RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
6
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19
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4.2k
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Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.2 years ago by ▴ 690 • written 7.2 years ago by ▴ 50
5 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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