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TranscriptDb and genomicranges questions
Cancer TranscriptDb Category IRanges GenomicRanges Cancer TranscriptDb Category IRanges
15.2 years ago Hervé Pagès 16k
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1.7k
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append on DNAStringSet produces an empty DNAString as last element
Cancer Cancer
updated 15.2 years ago by 16k • written 15.2 years ago by ▴ 20
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flowStats Plot quadrantGate Filter Result Smooth=FALSE
Cancer flowStats Cancer flowStats
15.2 years ago Chao-Jen Wong ▴ 580
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2
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1.3k
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Quality control on Human Affymetrix Exon microarrays
GO Cancer probe affyQCReport GO Cancer probe affyQCReport
updated 15.2 years ago by ★ 13k • written 15.2 years ago by ★ 1.9k
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819
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xps: RMA background plot using ROOT graphics
Cancer xps Cancer xps
updated 15.2 years ago by ★ 3.9k • written 15.2 years ago by ★ 1.9k
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Bioconductor Digest, Vol 90, Issue 1
Cancer probe limma Cancer probe limma
15.2 years ago Amos Folarin ▴ 20
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2.0k
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Postdoctoral positions at Harvard
Genetics Cancer Yeast Genetics Cancer Yeast
15.2 years ago Edo Airoldi ▴ 10
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898
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FW: Software engineer/application developer position
Cancer Cancer
15.2 years ago John Zhang ★ 2.9k
0
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1
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1.6k
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write.XStringView/write.XStringSet highly inefficient (solved)
Cancer BSgenome PROcess GLAD BSgenome Cancer BSgenome PROcess GLAD BSgenome
updated 15.2 years ago by ★ 13k • written 15.2 years ago by ▴ 550
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641
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problem using Alternative CDF environments, CdfEnvAffy
Cancer Cancer
15.2 years ago Hervé Pagès 16k
0
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1
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664
views
In limma, how to set quility weight for each spot.
Cancer limma Cancer limma
updated 15.2 years ago by 21k • written 15.2 years ago by ▴ 190
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4
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1.4k
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Performing set ops with an IRanges object loaded with elementMetadata is like a shotgun, pointing at my foot.
Cancer IRanges Cancer IRanges
updated 15.3 years ago by ★ 11k • written 15.3 years ago by ★ 13k
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4
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1.4k
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Limma for GoldenGate Methylation Cancer Panel I
Cancer limma Cancer limma
15.3 years ago Jinyan Huang ▴ 50
0
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2
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1.6k
views
error/problem with biomaRt gene symbol query
Microarray Cancer probe biomaRt ASSIGN Microarray Cancer probe biomaRt ASSIGN
updated 15.3 years ago by ▴ 500 • written 15.3 years ago by ▴ 100
0
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2
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1.6k
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error from rsamtools on 1000 genomes
Cancer HapMap Rsamtools genomes Cancer HapMap Rsamtools genomes
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 100
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1.9k
views
Which package for gene expression correlation analysis
Cancer affy Cancer affy
15.3 years ago Naomi Altman ★ 6.0k
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1.1k
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limma matrix design for biological replicates.
Cancer Breast limma Cancer Breast limma
15.3 years ago Gordon Smyth 53k
0
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884
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limma matrix design for biological replicates.
Cancer Breast limma Cancer Breast limma
15.3 years ago neeraj rana ▴ 100
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2
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1.3k
views
Querying/manipulating JASPAR data
Transcription Cancer Transcription Cancer
updated 15.3 years ago by ★ 1.7k • written 15.3 years ago by ★ 13k
0
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1
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1.7k
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How to cluster genes based on their GO term in Arabidopsis?
GO Cancer Prostate goProfiles GO Cancer Prostate goProfiles
updated 15.3 years ago by 68k • written 15.3 years ago by ▴ 280
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1.2k
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flowStats: lymphGate Issue, plotting the results?
Cancer flowStats Cancer flowStats
15.3 years ago Chao-Jen Wong ▴ 580
0
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3
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1.9k
views
identical output plots for NUSE AND RLE
GO Cancer affyPLM GO Cancer affyPLM
updated 15.3 years ago by ▴ 320 • written 15.3 years ago by ★ 2.0k
0
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1
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1.6k
views
question on makeTranscriptDbFromUCSC
Cancer rtracklayer GenomicRanges PING SANTA Cancer rtracklayer GenomicRanges PING SANTA
updated 15.3 years ago by ▴ 10 • written 15.3 years ago by 16k
0
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1
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1.3k
views
Error message with rmaMicroRna on mouse data in AgiMicroRNA
Cancer probe AgiMicroRna Cancer probe AgiMicroRna
updated 15.3 years ago by ▴ 360 • written 15.3 years ago by ★ 2.0k
0
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10
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2.5k
views
AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.
miRNA Microarray Cancer microRNA miRNA Microarray Cancer microRNA
15.3 years ago Neel Aluru ▴ 460
0
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0
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951
views
Error in cvArray in AgiMicroRNA
Cancer probe Cancer probe
15.3 years ago Richard Friedman ★ 2.0k
0
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0
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941
views
mvaPlots of RMA normalized data in AgiMicroRNA
Cancer AgiMicroRna Cancer AgiMicroRna
15.3 years ago Richard Friedman ★ 2.0k
0
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0
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692
views
Error Message upon filtering in AgiMicroRNA of RMA normalized object.
Cancer Cancer
15.3 years ago Richard Friedman ★ 2.0k
0
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0
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752
views
Biostrings_2.16.5 / IRanges_1.7.1 :: Broken(?) -- DISREGARD
Cancer Biostrings IRanges Cancer Biostrings IRanges
15.3 years ago Steve Lianoglou ★ 13k
0
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728
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Biostrings_2.16.5 / IRanges_1.7.1 :: Broken(?)
Cancer Cancer
15.3 years ago Steve Lianoglou ★ 13k
0
votes
2
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1.1k
views
Error message with rmaMicroRna on mouse data in AgiMicroRNA
Cancer probe Cancer probe
updated 15.3 years ago by ▴ 360 • written 15.3 years ago by ★ 2.0k
0
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1
reply
1.7k
views
TLDA data
Clustering Cancer PROcess cycle HTqPCR Clustering Cancer PROcess cycle HTqPCR
updated 15.3 years ago by ★ 2.0k • written 15.3 years ago by ▴ 40
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0
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905
views
AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.
miRNA Microarray Cancer microRNA miRNA Microarray Cancer microRNA
15.3 years ago Richard Friedman ★ 2.0k
0
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0
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822
views
DAVIDQuery
Cancer DAVIDQuery Cancer DAVIDQuery
15.3 years ago Day, Roger S ▴ 60
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2
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2.4k
views
GEOquery Meta
Cancer Prostate Cancer Prostate
updated 15.4 years ago by 21k • written 15.4 years ago by ▴ 340
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1
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1.1k
views
Trouble with maQualityPlots
Cancer Cancer
updated 15.4 years ago by 68k • written 15.4 years ago by ▴ 10
0
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4
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972
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Error Message with RMA normalization in AgiMicroRNA
Cancer Cancer
updated 15.4 years ago by 68k • written 15.4 years ago by ★ 2.0k
0
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3
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2.7k
views
Reading in data with HTqPCR
Cancer cycle Cancer cycle
updated 15.4 years ago by ▴ 40 • written 15.4 years ago by ★ 2.0k
0
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1
reply
1.0k
views
error message in cvArray command in AgiMicroRna
Cancer Cancer
updated 15.4 years ago by ▴ 460 • written 15.4 years ago by ★ 2.0k
0
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0
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1.7k
views
Two Bioconductor Job Opportunities in Seattle
Microarray Annotation Cancer cdf Microarray Annotation Cancer cdf
15.4 years ago Martin Morgan 25k
0
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0
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577
views
GCRMA Normalization Differences between Windows and MAC
Cancer Cancer
15.4 years ago Pierre Gestraud ▴ 10
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0
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1.4k
views
Experimental design for RNA-Seq
Sequencing qPCR Cancer Sequencing qPCR Cancer
15.4 years ago Jakob Hedegaard ▴ 170
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1
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1.2k
views
Difficulty installing oneChannelGUI in Vista
Cancer affylmGUI oneChannelGUI Cancer affylmGUI oneChannelGUI
updated 15.4 years ago by 68k • written 15.4 years ago by ★ 2.0k
0
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1
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1.4k
views
is database RefSeq achievable from any Bioconductor package
Annotation Cancer biomaRt GenomicFeatures Annotation Cancer biomaRt GenomicFeatures
updated 15.4 years ago by ★ 6.5k • written 15.4 years ago by ★ 13k
0
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4
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1.8k
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Reading in data with HTqPCR
qPCR Cancer cycle HTqPCR qPCR Cancer cycle HTqPCR
15.4 years ago Heidi Dvinge ★ 2.0k
0
votes
0
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688
views
Collaborators
Microarray Clustering Cancer Ovarian Microarray Clustering Cancer Ovarian
15.4 years ago Alexandru Floares ▴ 10
0
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0
replies
763
views
11 more packages available on 64-bit Windows
Cancer Cancer
15.4 years ago Hervé Pagès 16k
0
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1
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1.3k
views
sir
Cancer cycle HTqPCR Cancer cycle HTqPCR
updated 15.4 years ago by ▴ 40 • written 15.4 years ago by ★ 2.0k
0
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0
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1.3k
views
SPIA package problem
Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism
15.4 years ago January Weiner ▴ 370
0
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2
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1.0k
views
Error: formal argument "envir" matched by multiple actual arguments
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
updated 15.4 years ago by ▴ 30 • written 15.4 years ago by 25k
1,555 results • Page 14 of 32
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
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Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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