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[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
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updated 9.3 years ago by ▴ 370 • written 10.4 years ago by ▴ 160
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9.6 years ago patrick.schordert ▴ 30
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convert data in to expression set
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updated 10.9 years ago by ▴ 180 • written 10.9 years ago by ▴ 80
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updated 12.5 years ago by ★ 3.3k • written 12.5 years ago by ▴ 360
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Converting single GRanges object as per chromosome GRangeList
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updated 10.4 years ago by ★ 13k • written 10.4 years ago by ▴ 260
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getLDS error in scan
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updated 3.5 years ago by ★ 6.5k • written 3.5 years ago by • 0
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handling 12 bit tiffs in EBImage
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updated 13.9 years ago by ▴ 310 • written 13.9 years ago by ▴ 120
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Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
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5 months ago j_denton • 0
2
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Using oligo or xps to read and convert RNA-seq data CEL file to txt file.
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updated 9 months ago by 65k • written 9 months ago by • 0
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Converting to official gene symbols
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updated 15.8 years ago by ▴ 20 • written 15.8 years ago by ▴ 90
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Apply non-Gaussian distribution data to limma
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updated 10.4 years ago by 65k • written 10.4 years ago by ★ 13k
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minfi, bumphunter + complex experimental design, and 3 other 450K queries
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updated 8.3 years ago by ▴ 30 • written 9.9 years ago by ★ 3.9k
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RNA-seq analysis using R
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updated 12 months ago by 50k • written 5.4 years ago by • 0
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Can XCMS output continuum/profile data to netCDF format?
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updated 7.4 years ago by ★ 2.0k • written 7.4 years ago by • 0
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Pan-organism OrgDb database, Accession number translated to organism name in R
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updated 5 months ago by 65k • written 5 months ago by • 0
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Mapping gene symbols to gene names (org.Hs.eg.db?)
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updated 10.0 years ago by 65k • written 10.0 years ago by ★ 1.1k
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RleList
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updated 10.3 years ago by ★ 11k • written 10.3 years ago by ▴ 20
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updated 8.3 years ago by 65k • written 8.3 years ago by • 0
1
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converting amino-acid one letter code into cDNA sequene
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7.9 years ago arvind90.psc • 0
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How to convert Illumina HT_12_v4 annotation
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updated 16 months ago by ▴ 20 • written 6.4 years ago by • 0
1
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MethyLumiSet object
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11.1 years ago Tim Triche ★ 4.2k
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GenBank RefSeq conversion
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updated 15.9 years ago by 21k • written 15.9 years ago by ▴ 150
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Rsubread for paired end SOLID sequencing
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updated 10.7 years ago by ★ 3.6k • written 10.7 years ago by ▴ 50
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making ExpressionSet from RGList via NChannelSet for use with 'sva'
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updated 8.1 years ago by 50k • written 8.1 years ago by • 0
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3
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To convert MAList to ExpressionSet using R package 'convert'
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updated 7.5 years ago by 50k • written 7.5 years ago by • 0
0
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GenMAPP swissprot question / answers
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20.6 years ago Phguardiol@aol.com ▴ 720
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Re: Bioconductor Digest, Vol 6, Issue
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20.7 years ago Leslie Cope ▴ 50
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Re: how to convert expression set data into matrix data ?
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20.7 years ago Sylvia Merk ▴ 50
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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)
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updated 16 months ago by 50k • written 11.9 years ago by ★ 6.5k
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Re: time serie data
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20.6 years ago Nicholas Lewin-Koh ▴ 430
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How to convert Illumina ProbeIDs to nuIDs without nuID indexed annotation libraries?
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updated 15.6 years ago by ★ 1.2k • written 15.6 years ago by ▴ 150
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how to convert expression set data into matrix data ?
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updated 20.7 years ago by ▴ 920 • written 20.7 years ago by ▴ 10
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multtest question
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updated 21.1 years ago by ★ 2.3k • written 21.1 years ago by ▴ 720
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Genomicfeatures chromosome names matching
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12.2 years ago Hervé Pagès 16k
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Importing data into Bioconductor
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21.3 years ago Fernando Henrique Ferraz P da Rosa ▴ 20
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question subsetting expressionSet
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updated 12.3 years ago by ▴ 550 • written 12.3 years ago by ★ 3.9k
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arrayQualityMetrics - how do I use this with an MAList object???
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updated 15.6 years ago by ▴ 680 • written 15.6 years ago by 25k
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summarizing probe intensites before or after normalization- 1. how to do with RMA 2. Opinions?
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17.6 years ago James W. MacDonald 65k
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Affy : checkSlotAssignment() Error
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21.5 years ago Sundaram, Shyam NIH/CIT ▴ 110
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RE: venn diagram
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updated 20.0 years ago by ▴ 620 • written 20.0 years ago by ▴ 20
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reading in a text file
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updated 20.2 years ago by ▴ 60 • written 20.2 years ago by ▴ 30
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10.0 years ago Luo Weijun ★ 1.6k
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fastq files
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updated 13.1 years ago by 25k • written 13.1 years ago by ▴ 860
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Re: affylmGUI
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19.9 years ago James Wettenhall ▴ 1000
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qvalues, sam, limma
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19.9 years ago Naomi Altman ★ 6.0k
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19.8 years ago s-uchida ▴ 20
0
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Re: [R] How to convert a vector into a list
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19.7 years ago Adaikalavan Ramasamy ★ 1.8k
0
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Annotate Package: How do I get the gene names and how do I write my matrix
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19.7 years ago James W. MacDonald 65k
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installing affy devel package
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20.2 years ago Ben Bolstad ★ 1.1k
50 results • Page 1 of 1
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 30
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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