0
votes
2
replies
1.7k
views
Drastic change in edgeR p-value calculation?
edgeR edgeR
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 10
0
votes
1
reply
1.3k
views
pamr
pamr pamr
updated 13.0 years ago by 68k • written 13.0 years ago by ▴ 10
0
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0
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Fwd: rTANDEM package -- An R encapsulation of the X!Tandem algorithm
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13.0 years ago Frederic Fournier ▴ 40
0
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0
replies
1.1k
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Diffbind error
DiffBind DiffBind
13.0 years ago José Luis Lavín ▴ 280
2
votes
3
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1.7k
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rTANDEM package -- An R encapsulation of the X!Tandem algorithm
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updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 40
0
votes
0
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Fwd: ExomeCopy package error
Sequencing exomeCopy Sequencing exomeCopy
13.0 years ago love ▴ 150
0
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5
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How to deal with SNPs in microarray
Microarray Microarray
updated 13.0 years ago by 21k • written 13.0 years ago by ▴ 50
0
votes
0
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Why does a call to "unique" removes a DNAStringSet names?
Cancer Cancer
13.0 years ago Hervé Pagès 16k
0
votes
2
replies
2.5k
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biomaRt and RCurl
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updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 10
0
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0
replies
1.4k
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ExomeCopy package error
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13.0 years ago Guest User ★ 13k
0
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0
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1.1k
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Web Developer/Programmer Position at Harvard Medical School
13.0 years ago Daniels, Jena Eve ▴ 10
0
votes
0
replies
768
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lumi NuID to UCSC, for example "xl5dFtdFTQCRSSkbwc" to something like "uc002qsd.4"
lumi lumi
13.0 years ago Fenton Christopher Graham ▴ 90
0
votes
0
replies
1.4k
views
correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
13.0 years ago Robert Castelo ★ 3.4k
0
votes
1
reply
1.1k
views
limma time-course dependent data
limma limma
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 50
0
votes
1
reply
1.3k
views
edgeR 3.0.6: Possible (small) bug in glmLRT when passing contrasts?
Cancer edgeR Cancer edgeR
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 30
0
votes
6
replies
2.0k
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pileupAsGRanges depth limit
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updated 13.0 years ago by 25k • written 13.0 years ago by ★ 1.1k
0
votes
0
replies
1.8k
views
Problem to download Kegg map from KEGGprofile package
GO KEGGprofile GO KEGGprofile
13.0 years ago gregory voisin ▴ 430
0
votes
0
replies
734
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Windows or Excel to R txt file
13.0 years ago TriS ▴ 200
0
votes
0
replies
1.0k
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EBcoexpress package
13.0 years ago TriS ▴ 200
0
votes
2
replies
1.3k
views
correlation between two pathways' genes
Pathways Pathways
updated 13.0 years ago by ★ 1.3k • written 13.0 years ago by ▴ 440
0
votes
2
replies
1.7k
views
EdgeR estimateTagwiseDisp()
Alignment edgeR Alignment edgeR
updated 13.0 years ago by 53k • written 13.0 years ago by ★ 13k
0
votes
5
replies
2.0k
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filtering before using DESeq
DESeq DESeq
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 190
0
votes
2
replies
1.6k
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coXpress package
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ▴ 200
0
votes
3
replies
3.1k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 13.0 years ago by 25k • written 13.0 years ago by ▴ 310
0
votes
2
replies
1.4k
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warning during installation of cummeRbund
cummeRbund cummeRbund
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ▴ 20
0
votes
8
replies
2.9k
views
vmatchPDict?
BSgenome probe BSgenome BSgenome probe BSgenome
updated 13.0 years ago by 16k • written 13.0 years ago by ▴ 130
0
votes
4
replies
3.2k
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Oligo package annotation
updated 13.0 years ago by 68k • written 13.0 years ago by ★ 13k
0
votes
1
reply
1.3k
views
trouble with installing biomaRt in R-2.15
biomaRt biomaRt
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 190
0
votes
6
replies
2.9k
views
Different number of genes when using HTseq and cuffdiff
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 260
0
votes
0
replies
1.4k
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RankProd absurd results
qPCR RankProd qPCR RankProd
13.0 years ago Guest User ★ 13k
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0
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Large datasets in methylumi
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13.0 years ago Guest User ★ 13k
2
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6
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3.6k
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all human gene coordinates
13.1 years ago • updated 13.0 years ago Wim Kreinen ▴ 100
0
votes
1
reply
1.6k
views
Anova for microarrays
Microarray Microarray
updated 13.0 years ago by 68k • written 13.0 years ago by ▴ 20
0
votes
2
replies
1.2k
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can't install "goseq" through BioC
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ▴ 410
0
votes
4
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1.3k
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DEXSeq all p-values are 1
GO DEXSeq GO DEXSeq
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ★ 13k
0
votes
3
replies
2.1k
views
access R server via Amazon Web Services.
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ▴ 430
0
votes
3
replies
1.4k
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need help regarding microarray data analysis using limma
updated 13.0 years ago by ★ 1.9k • written 13.0 years ago by ▴ 20
0
votes
3
replies
1.6k
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bam file in easyRNASeq
updated 13.0 years ago by ★ 1.2k • written 13.0 years ago by ▴ 80
0
votes
9
replies
5.2k
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Exclude overlapping intervals
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ▴ 110
0
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0
replies
1.2k
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tools for function enrichment analysis
Annotation Annotation
13.0 years ago Abhishek Pratap ▴ 410
0
votes
3
replies
3.8k
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RNA-seq, low count filtering and multiple testing
edgeR edgeR
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 120
0
votes
0
replies
579
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Fwd: Highly Expressed Genes among DE genes in edgeR
13.0 years ago Shreyartha Mukherjee ▴ 80
0
votes
4
replies
3.6k
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convert gene name to Affy ID
Preprocessing Preprocessing
updated 13.0 years ago by ▴ 10 • written 13.0 years ago by ★ 13k
0
votes
1
reply
983
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Highly Expressed Genes among DE genes in edgeR
updated 13.0 years ago by ★ 7.9k • written 13.0 years ago by ▴ 260
0
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0
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Job postings - computational biologists in translational science
Sequencing Cancer Sequencing Cancer
13.0 years ago Crispin Miller ★ 1.1k
0
votes
0
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2013***R Courses*** by XLSolutions Corp at 9 USA Cities: San Francisco, New York, Washington DC, Houston, Boston, Las Vegas, Seattle, etc
Clustering Clustering
13.0 years ago sue@xlsolutions-corp.com ▴ 570
0
votes
3
replies
2.3k
views
Use ChIPpeakAnno to find two-sided nearest genes to a peak
AnnotationData annotate ChIPpeakAnno AnnotationData annotate ChIPpeakAnno
13.0 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
450
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suggest/depends cleanup
updated 13.0 years ago by 68k • written 13.0 years ago by ★ 13k
0
votes
12
replies
2.9k
views
justRMA?
cdf probe cdf probe
updated 13.0 years ago by 68k • written 13.0 years ago by ▴ 70
0
votes
0
replies
880
views
Correct data analysis with siggenes
Microarray Microarray
13.0 years ago Marco Ortiz ▴ 10
46,699 results • Page 560 of 934
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Answer: Ensembl site unresponsive via biomaRt by horaortiz8 • 0
I appreciate the link. I'll get in touch with them directly; I wish they had a status page of some kind. https://www.ensembl.org/Help/Cont…
Comment: segfault in edgeR glmQLFit by Mark • 0
Thanks! We had been considering some of these adjustments as well, given the small number of features and total reads. Your advice is well-…
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ATpoint ★ 5.0k
> and I first used the normalized counts You would not use these normalized counts for PCA as they're not on log2 scale. As such, the feat…
Comment: EuroBioC2026 abstract submission is open! by TikTsokaasocissalpc • 0
Submitting abstracts for EuroBioC2026 can be exciting but organizing ideas is key. A Random Word Generator [visit][1] can help create uniqu…
Comment: DESeq2 on non-RNASeq counts data by TikTsokaasocissalpc • 0
In data analysis, behavior differences based on data type are common. Similarly, Best EDI Software adapts to non-standard transaction volum…
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C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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