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ChIPpeakAnno: Inquiry for Worm Analysis
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13.9 years ago • updated 13.8 years ago Julie Zhu ★ 4.3k
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1
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1.5k
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Problems installing EBImage package
convert EBImage convert EBImage
updated 13.8 years ago by ★ 13k • written 13.8 years ago by ★ 13k
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Adjacency to network using R
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updated 13.8 years ago by ★ 4.2k • written 13.8 years ago by ▴ 120
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problems generating a gene2GOlist in topGO
Genetics Annotation GO hgu95av2 convert biomaRt topGO Genetics Annotation GO hgu95av2
updated 13.8 years ago by ▴ 400 • written 13.8 years ago by ▴ 510
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1.4k
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GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa
convert gage convert gage
updated 13.8 years ago by ★ 1.6k • written 13.9 years ago by ▴ 200
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3
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A question about MA and RG lists and normalization with two channel agilent arrays.
convert convert
updated 13.8 years ago by ▴ 390 • written 13.8 years ago by ▴ 90
0
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655
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ChipPeakAnno question about file conversion
convert ChIPpeakAnno convert ChIPpeakAnno
13.8 years ago Julie Zhu ★ 4.3k
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11
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creating GRanges and reading BAM files
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updated 13.8 years ago by ▴ 80 • written 13.9 years ago by ▴ 70
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Coverage Question: GenomicRanges
Coverage convert Coverage convert
updated 13.8 years ago by ★ 11k • written 13.8 years ago by ▴ 250
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4
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ChIPpeakAnno as.data.frame error
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updated 13.9 years ago by ★ 4.3k • written 13.9 years ago by ▴ 910
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arrayQualityMetrics error with MAList
convert arrayQualityMetrics convert arrayQualityMetrics
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 10
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arrayQualityMetrics package - bugs and errors
limma affyPLM convert arrayQualityMetrics limma affyPLM convert arrayQualityMetrics
13.9 years ago Wolfgang Huber ★ 13k
0
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IlluminaMousev2.db probe quality information questions?
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13.9 years ago Mark Dunning ★ 1.1k
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GAGE Package: Problem with "Affymetrix hg u133 plus 2 probeset IDs" conversion to Gene names or vice versa
convert gage convert gage
13.9 years ago Javerjung Sandhu ▴ 200
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1
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1.6k
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GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
convert gage convert gage
13.9 years ago Javerjung Sandhu ▴ 200
0
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convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
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13.9 years ago delhomme@embl.de ★ 1.2k
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Help with promoter analysis
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13.9 years ago Davy ▴ 20
0
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convert "Genome_intervals_stranded" to "Genome_intervals"? (girafe)
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13.9 years ago karlerhard@berkeley.edu ▴ 60
0
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1
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1.2k
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IlluminaMousev2.db probe quality information questions?
probe convert probe convert
13.9 years ago Lourdes Peña Castillo ▴ 140
0
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using easyRNASeq examples
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13.9 years ago delhomme@embl.de ★ 1.2k
0
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1
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1.7k
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how can i convert a gse object(expression sets) to affybatch
convert GEOquery convert GEOquery
updated 13.9 years ago by 21k • written 13.9 years ago by ▴ 100
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8
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DESeq and transcript-wise analysis
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13.9 years ago Elena Sorokin ▴ 160
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Genomicfeatures chromosome names matching
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13.9 years ago Hervé Pagès 16k
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7
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Limma question_Intra-Spot Correlation Question
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updated 13.9 years ago by 53k • written 13.9 years ago by ▴ 30
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create GeneSetCollection from OBOCollection
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13.9 years ago Marc Carlson ★ 7.2k
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converting transcripts to gene level
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updated 13.9 years ago by ★ 11k • written 13.9 years ago by ▴ 410
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converting intensity values to log ratios?
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13.9 years ago James W. MacDonald 68k
0
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1
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refseq to genesymbol with BiomaRt - problem occurs
GO hgu133plus2 PROcess convert biomaRt GO hgu133plus2 PROcess convert biomaRt
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 240
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converting intensity values to log ratios?
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14.0 years ago Mark Baumeister ▴ 40
0
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1
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972
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Strecth of N's in between reads
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updated 14.0 years ago by 21k • written 14.0 years ago by ▴ 120
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create GeneSetCollection from OBOCollection
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14.0 years ago Wendy Qiao ▴ 360
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writing BAM files from within R
convert Rsamtools convert Rsamtools
updated 14.0 years ago by ★ 6.8k • written 14.0 years ago by ▴ 10
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htSeqTools: using GRanges and GRangesList
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14.0 years ago Oscar Reina ▴ 20
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Saureus Affy Chip
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updated 14.0 years ago by ★ 7.2k • written 14.0 years ago by ▴ 200
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question subsetting expressionSet
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updated 14.0 years ago by ▴ 550 • written 14.0 years ago by ★ 4.1k
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GB_ACC to Entrez ids
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updated 14.0 years ago by 6.7k • written 14.0 years ago by ▴ 570
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Help on alternative and efficient data frame manipulation
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updated 14.0 years ago by ★ 13k • written 14.0 years ago by ★ 4.3k
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Combining raw images and locs files from different scans
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updated 14.1 years ago by ★ 6.6k • written 14.1 years ago by ▴ 350
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Extracting PROBE_ID from lumiBatch
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14.1 years ago Pan Du ▴ 440
0
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deqseq_count and BWA-based SAM files
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updated 14.1 years ago by ▴ 70 • written 14.1 years ago by ★ 13k
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ddCt isn't working with exported ABI7500-RT-PACR file
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updated 14.1 years ago by ▴ 300 • written 14.1 years ago by ▴ 20
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GRanges - coercion from dataframe
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14.1 years ago Fahim Md ▴ 250
0
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diagnosing problems with processing microarray data using lumi package
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14.2 years ago Juliet Hannah ▴ 360
3
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convert GeneSetCollection to a list
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updated 14.2 years ago by ★ 3.4k • written 14.2 years ago by ▴ 360
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DESeq - read counts
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updated 14.2 years ago by ★ 13k • written 14.2 years ago by ▴ 10
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Customizing gplots heatmap.2 - color range for heatmap and legend for RowSideColors
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14.2 years ago Chao-Jen Wong ▴ 580
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R/Bioconductor CDF to Affymetrix CDF
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updated 14.2 years ago by ▴ 10 • written 14.2 years ago by ▴ 830
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present / absent calls and detection p-values
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updated 14.3 years ago by ★ 3.6k • written 14.3 years ago by ▴ 340
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problem with frma( )
convert frma convert frma
updated 14.3 years ago by ▴ 830 • written 14.3 years ago by ▴ 20
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[Bioc-sig-seq] first remove low quality or adaptor
Cancer Biostrings convert Cancer Biostrings convert
updated 14.3 years ago by ★ 2.0k • written 14.3 years ago by 16k
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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