Showing : ttest • reset
5
votes
7
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3.4k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 10
0
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3
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1.6k
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apply Kruskall or other non-parametric test for multiple comparisons
r kruskal ttest nonparametric
7.1 years ago bhgyu ▴ 30
1
vote
3
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1.8k
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Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.3 years ago lirongrossmann ▴ 80
7
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11
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4.1k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq dmr ttest pvalue
updated 8.9 years ago by 67k • written 8.9 years ago by ▴ 660
4 results • Page 1 of 1
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Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
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…
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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