Showing : microarray • reset
0
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3
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limma and Volcano Plots
Microarray Proteomics Cancer PROcess Microarray Proteomics Cancer PROcess
updated 11.8 years ago by 53k • written 11.8 years ago by ▴ 130
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1.6k
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Pathview with minor species
Microarray Annotation Bacillus subtilis gage pathview Microarray Annotation gage pathview
11.8 years ago Luo Weijun ★ 1.6k
2
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5
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16k
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Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 11.9 years ago by 68k • written 11.9 years ago by ▴ 390
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6
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5.5k
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Question about quantile normalization and NA value
Microarray Normalization limma Microarray Normalization limma
updated 11.9 years ago by ▴ 20 • written 11.9 years ago by ▴ 10
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1
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2.2k
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fRMA for Gene ST arrays
Microarray probe oligo frma Microarray probe oligo frma
updated 11.9 years ago by ▴ 830 • written 11.9 years ago by ▴ 10
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4
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3.5k
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Missing probesets when creating Affymetrix GeneChip miRNA 4.0 CDF package using makecdfenv package
miRNA Microarray cdf makecdfenv miRNA Microarray cdf makecdfenv
updated 11.9 years ago by 68k • written 11.9 years ago by ★ 13k
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1
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3.3k
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limma - normalizeBetweenArrays function
Microarray limma Microarray limma
updated 11.9 years ago by 53k • written 11.9 years ago by ▴ 10
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0
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1.9k
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EximiR - Limma - miRCURY LNA - Exiqon
miRNA Microarray Cancer limma lumi ExiMiR miRNA Microarray Cancer limma lumi ExiMiR
11.9 years ago Paolo Kunderfranco ▴ 350
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1.6k
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Job opening: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital, Boston, MA, USA
Sequencing Microarray Cancer Sequencing Microarray Cancer
11.9 years ago Wittner, Ben ▴ 290
0
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1
reply
1.3k
views
GAGE analysis
Microarray gage Microarray gage
updated 11.9 years ago by ★ 1.6k • written 11.9 years ago by ▴ 130
0
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1
reply
2.6k
views
Importing RMA processed data into limma for eBayes
Microarray Normalization affy vsn limma PROcess xps Microarray Normalization affy vsn
11.9 years ago Matthew Thornton ▴ 390
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0
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1.6k
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OMICtools: An informative directory for HTS and array analysis
Microarray Microarray
12.0 years ago Guest User ★ 13k
0
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1
reply
3.1k
views
annotation package for HuEx-1_0-st-v1 platform instead of pd.huex.1.0.st.v1
Microarray Annotation hgu133a hgu133plus2 cdf Microarray Annotation hgu133a hgu133plus2
updated 12.0 years ago by ★ 3.9k • written 12.0 years ago by ▴ 10
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4
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2.9k
views
Limma, blocking, robust methods, and paired samples question
Microarray probe Microarray probe
updated 12.0 years ago by 53k • written 12.0 years ago by ▴ 440
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2
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2.2k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray DOSE Microarray DOSE
updated 12.0 years ago by ▴ 190 • written 12.0 years ago by ★ 13k
0
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0
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2.0k
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question about design for limma time course, 2 conditions and drug treatment microarray experiment
Microarray limma DOSE Microarray limma DOSE
12.0 years ago Gordon Smyth 53k
2
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2
replies
2.7k
views
[limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
Microarray Regression Microarray Regression
updated 12.0 years ago by 53k • written 12.0 years ago by ▴ 30
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5
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2.8k
views
Single-channel GenePix analysis with Limma (bg correction, normalization, weights)
Microarray Normalization vsn limma ASSIGN Microarray Normalization vsn limma ASSIGN
updated 12.1 years ago by 53k • written 12.1 years ago by ▴ 40
1
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4
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1.7k
views
distribution of agilent array data.‏
Microarray Normalization Microarray Normalization
updated 12.1 years ago by ▴ 70 • written 12.1 years ago by ▴ 100
0
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1
reply
1.5k
views
Random effect for RNAseq data in Limma package
RNASeq Microarray limma RNASeq Microarray limma
updated 12.1 years ago by 53k • written 12.1 years ago by ▴ 10
1
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0
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922
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distribution of agilent array data.
Microarray Normalization Microarray Normalization
12.1 years ago ccshao ▴ 70
0
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0
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1.1k
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New method for fully scalable preprocessing of large-scale gene expression atlases (RPA)
Microarray Preprocessing Microarray Preprocessing
12.1 years ago Leo Lahti ▴ 40
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1
reply
3.1k
views
Analysis of Human Gene 1.1 ST Array
Microarray cdf affy PROcess oligo xps Microarray cdf affy PROcess oligo xps
updated 12.1 years ago by 68k • written 12.1 years ago by ▴ 190
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2
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4.8k
views
Annotate - gene name to ENSEMBL
Microarray GO lumi Microarray GO lumi
updated 12.1 years ago by ▴ 400 • written 12.1 years ago by ▴ 180
0
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1
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1.4k
views
Fwd: [devteam-bioc] information about genefilter package
Microarray genefilter limma Microarray genefilter limma
updated 12.1 years ago by 68k • written 12.1 years ago by 16k
0
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1
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1.5k
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help with limma design, contrast matrices
Microarray limma Microarray limma
updated 12.1 years ago by ★ 7.9k • written 12.1 years ago by ▴ 50
0
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1.7k
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enrichment packages that accept t-stat (or related stat) as input
Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA
12.1 years ago Gordon Smyth 53k
0
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0
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1.4k
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enrichment packages that accept t-stat (or related stat) as input
Microarray Proteomics limma Category CAMERA GSVA Microarray Proteomics limma Category
12.1 years ago Pekka Kohonen ▴ 190
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10
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3.4k
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ANCOVA microarray time-course continuous & categorical variables / Limma extensions
RNASeq Microarray limma RNASeq Microarray limma
updated 12.1 years ago by 53k • written 12.1 years ago by ▴ 380
0
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0
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984
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analyses of CGH data
Microarray CGH Microarray CGH
12.1 years ago Isha Pandey Phd Scholar BITS Pilani Cam… ▴ 10
0
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1
reply
2.0k
views
arrayQualityMetrics - undefined columns selected
Microarray arrayQualityMetrics Microarray arrayQualityMetrics
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ▴ 50
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2
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3.6k
views
Biobase - Error: ExpressionSet
Microarray Annotation GO ExperimentData Biobase Microarray Annotation GO ExperimentData
updated 12.1 years ago by 1.6k • written 12.1 years ago by ▴ 50
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0
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4.7k
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
12.1 years ago Dan Tenenbaum ★ 8.2k
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Normalization before ComBat
Microarray Normalization probe affy frma Microarray Normalization probe affy frma
updated 12.1 years ago by ▴ 40 • written 12.2 years ago by ▴ 870
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How does one deal with spatial effects detected on single channel microarrays?
Microarray Normalization hu6800 affy gcrma marray nnNorm Harshlight Microarray hu6800
12.1 years ago Scott Robinson ▴ 130
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1.1k
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variation between chips - neqc()
Microarray Normalization probe limma lumi Microarray Normalization probe limma lumi
12.2 years ago Rao,Xiayu ▴ 550
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682
views
Overlapping region: Segment 0 error with processSwathData() for HumanHT12v4 microarray bead data
Microarray Microarray
12.2 years ago Alan Hutchison ▴ 10
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0
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911
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Fwd: Regarding miRNA analysis
miRNA Microarray miRNA Microarray
12.2 years ago deepika lakhwani ▴ 170
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1
reply
1.1k
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Regarding miRNA analysis
miRNA Microarray miRNA Microarray
12.2 years ago deepika lakhwani ▴ 170
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0
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1.2k
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Bioconductor/R workshop for high-throughput data analysis (web version)
Sequencing Microarray Sequencing Microarray
12.2 years ago gregory voisin ▴ 430
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1
reply
1.6k
views
Limma normalizeBetweenArrays does not normalize M values using Quantile method directly.???
Microarray limma Microarray limma
updated 12.2 years ago by 68k • written 12.2 years ago by ▴ 60
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2
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1.2k
views
problem with creating array annotation package
Microarray Annotation ChipName Microarray Annotation ChipName
updated 12.2 years ago by ★ 3.9k • written 12.2 years ago by ★ 4.1k
0
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2
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3.0k
views
Differential expression analysis in Limma for one factor after adjusting for a covariate
Microarray limma Microarray limma
updated 12.2 years ago by ▴ 120 • written 12.3 years ago by ▴ 300
0
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2
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1.5k
views
Agilent two color Quantile normalization
Microarray limma Microarray limma
updated 12.2 years ago by 68k • written 12.2 years ago by ▴ 60
0
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2
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1.2k
views
Regression Analysis
Microarray limma Microarray limma
updated 12.2 years ago by 21k • written 12.2 years ago by ▴ 150
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7
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5.5k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 12.2 years ago by ▴ 470 • written 12.2 years ago by ▴ 680
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2
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1.3k
views
Illumina based one color microarray data analysis
Microarray Clustering Microarray Clustering
updated 12.2 years ago by ★ 3.6k • written 12.3 years ago by ★ 13k
0
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0
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1.3k
views
Human Transcriptome Array 2.0 chip
Microarray affy Microarray affy
12.2 years ago Guest User ★ 13k
0
votes
2
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6.0k
views
sva + voom + limma
RNASeq Microarray sva RNASeq Microarray sva
updated 12.3 years ago by 53k • written 12.3 years ago by ▴ 120
0
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6
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2.2k
views
How does one deal with spatial effects detected on single channel microarrays?
Microarray Normalization affy marray nnNorm Microarray Normalization affy marray nnNorm
updated 12.3 years ago by ★ 3.9k • written 12.3 years ago by ★ 13k
2,319 results • Page 15 of 47
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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