Bioconductor Plotmds

Showing : plotmds • reset

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1.3k

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plotMDS limma

17 months ago • updated 16 months ago Cen • 0

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3.5k

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plotMDS limma

updated 18 months ago by Gordon Smyth 52k • written 18 months ago by liujy4 • 0

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1.6k

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plotMDS PCA RNASeq MDS

updated 2.7 years ago by Gordon Smyth 52k • written 2.8 years ago by Raito92 ▴ 60

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1.5k

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limma plotMDS

3.4 years ago jamie.gearing ▴ 60

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4.6k

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edgeR plotmds differential gene expression MDS mdsplot

updated 6.0 years ago by Gordon Smyth 52k • written 6.0 years ago by ilovesuperheroes1993 • 0

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874

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plotMDS Cell lines limma

updated 6.3 years ago by Gordon Smyth 52k • written 6.3 years ago by Alexander Azarian ▴ 30

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1.1k

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tree bootstrap dgelist plotmds

6.8 years ago Larry K. • 0

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6.5k

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limma edger plotmds tmm masigpro

7.0 years ago dacaba.92 ▴ 10

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1.8k

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edger plotmds

7.2 years ago fawazfebin ▴ 60

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2.2k

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edger plotmds

updated 7.2 years ago by Aaron Lun ★ 28k • written 7.2 years ago by mictadlo ▴ 10

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1.8k

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affymetrix microarrays sva combat sva batch effect plotMDS

updated 8.3 years ago by Jeff Leek ▴ 650 • written 8.3 years ago by svlachavas ▴ 840

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1.3k

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rgl plot3d plotmds

8.7 years ago Adam • 0

12 results • Page 1 of 1

Recent ...

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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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