Showing : microarray • reset
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Can I input ordinal variables into a model in Limma?
Microarray limma Microarray limma
updated 12.3 years ago by ▴ 130 • written 12.3 years ago by 53k
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1.7k
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microarray outlier detection
Microarray limma Microarray limma
12.3 years ago Gordon Smyth 53k
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2
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2.4k
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microarray outlier detection
Microarray Microarray
updated 12.3 years ago by ▴ 200 • written 12.3 years ago by ★ 13k
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908
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Can I input ordinal variables into a model in Limma?
Microarray limma Microarray limma
12.3 years ago Guest User ★ 13k
2
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2.3k
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Complex Limma design: technical replication, biological replication and repeated experiment
Microarray limma Microarray limma
12.3 years ago Gordon Smyth 53k
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1.1k
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Complex Limma design: technical replication, biological replication and repeated experiment
Microarray limma Microarray limma
12.3 years ago Guest User ★ 13k
0
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1
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894
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RMA probe summarization when sizes of probesets are unequal
Microarray Normalization probe oligo Microarray Normalization probe oligo
updated 12.3 years ago by 68k • written 12.3 years ago by ★ 13k
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898
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maskBAD package - Errors during creation of mask
Microarray probe maskBAD Microarray probe maskBAD
12.4 years ago Ron Rotkopf ▴ 10
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4
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2.2k
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DexSeq extracols option
RNASeq Microarray Genetics Annotation Normalization Infrastructure Cancer probe limma
updated 12.4 years ago by ★ 1.9k • written 12.4 years ago by ▴ 40
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1.2k
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Suggestion - gene set enrichment of genes against BP and Disease gene sets
Microarray PROcess Microarray PROcess
12.4 years ago Bade ▴ 310
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1.6k
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Job reminder: Open position for a Core Bioinformatician in Lund, Sweden
Microarray BRAIN Microarray BRAIN
12.4 years ago _Bio - Informatics ▴ 20
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977
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Vector for Targest in Tquantile Normalization for different groups
Microarray Normalization Microarray Normalization
12.4 years ago Gordon Smyth 53k
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830
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cyber-T error
Microarray Microarray
12.4 years ago Matthew McCormack ▴ 180
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12
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3.1k
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RNAseq machine learning classifier
RNASeq Microarray RNASeq Microarray
updated 12.4 years ago by ▴ 60 • written 12.4 years ago by ▴ 380
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2
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1.5k
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limma for homemade microarray - question on NAs and multiple probes for one gene
Microarray Normalization GO Network Cancer probe limma Microarray Normalization GO probe
updated 12.4 years ago by 53k • written 12.4 years ago by ★ 3.0k
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1.3k
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symbol and filtering -affy hugene ST 1.0 -oligo limma
Microarray limma Microarray limma
12.4 years ago Rao,Xiayu ▴ 550
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5
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1.9k
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limma for homemade microarray - question on NAs and multiple probes for one gene
Microarray Microarray
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 50
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5
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2.0k
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Illumina Probe_ID used in the LIMMA package for neqc function
Microarray Annotation Normalization Clustering probe limma Microarray Annotation probe
updated 12.4 years ago by ▴ 40 • written 12.4 years ago by ★ 3.6k
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1.2k
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illumina microarray and affymetrix exon array data
Microarray affy Microarray affy
12.4 years ago Rao,Xiayu ▴ 550
0
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1
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992
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comBat or PCA to adjust for hidden variables in a high-throughput qPCR experiment with only 120 genes measured
Microarray Microarray
12.4 years ago shirley zhang ★ 1.0k
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1.4k
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Open position for a Core Bioinformatician in Lund, Sweden
Microarray BRAIN Microarray BRAIN
12.4 years ago _Bio - Informatics ▴ 20
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4
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1.9k
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read.ilmn() and variation between chips
Microarray Normalization probe limma Microarray Normalization probe limma
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 550
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1
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1.1k
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What is the FDR set to for the BH method.
Microarray Microarray
updated 12.4 years ago by ★ 6.0k • written 12.4 years ago by ▴ 50
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1
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2.4k
views
Illumina Probe_ID used in the LIMMA package for neqc function
Microarray Annotation probe limma Microarray Annotation probe limma
updated 12.4 years ago by ★ 3.6k • written 12.4 years ago by ▴ 40
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17
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3.6k
views
IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
Microarray illuminaHumanv2 Microarray illuminaHumanv2
updated 12.4 years ago by ★ 4.2k • written 12.4 years ago by ▴ 190
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753
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sample probe profile or sample gene profile
Microarray probe Microarray probe
12.4 years ago Guest User ★ 13k
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3
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1.2k
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read.ilmn() and variation between chips
Microarray Normalization limma Microarray Normalization limma
updated 12.4 years ago by 53k • written 12.4 years ago by ▴ 550
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1.8k
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How to filter genes not expressed in all arrays using limma (single channel agilent microarray data)
Microarray Microarray
12.4 years ago Guest User ★ 13k
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0
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1.1k
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comBat or PCA to adjust for hidden variables in qPCR data
Microarray Microarray
12.4 years ago shirley zhang ★ 1.0k
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1.6k
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Job opening: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital & Harvard Medical School
Sequencing Microarray Cancer Sequencing Microarray Cancer
12.4 years ago Wittner, Ben ▴ 290
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1.1k
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illumina microarray analysis questions (limma and heatmap)
Microarray Normalization probe limma Microarray Normalization probe limma
12.4 years ago Rao,Xiayu ▴ 550
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5
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2.1k
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ERCC spike-in probes in
Microarray Normalization cdf affy Microarray Normalization cdf affy
updated 12.4 years ago by 68k • written 12.4 years ago by ★ 13k
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4
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2.1k
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FeatureExpressionSet using list.files() in place of read.xysfiles()
Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ▴ 140
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1.0k
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why could I only get two different expressed genes by Limma?
Microarray Annotation Cancer Microarray Annotation Cancer
updated 12.5 years ago by ▴ 310 • written 12.5 years ago by ▴ 10
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1.0k
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using limma to analyze microarray data
Microarray limma Microarray limma
12.5 years ago Guest User ★ 13k
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1.3k
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ComBat function (sva) generates very low adjusted p.values for a big number of genes
Microarray Normalization Clustering limma sva Microarray Normalization Clustering limma
12.5 years ago Alexandra Popa ▴ 10
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913
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detectionCall usefulness
Microarray Microarray
updated 12.5 years ago by ▴ 440 • written 12.5 years ago by ★ 13k
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10
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3.8k
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PAIR files -- feature set table
Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism
updated 12.5 years ago by ★ 4.3k • written 12.5 years ago by ★ 13k
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3.2k
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Filtering is not recommended with LIMMA?
Microarray Preprocessing limma Microarray Preprocessing limma
12.5 years ago Gordon Smyth 53k
0
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0
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1.9k
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request on negative values after 'sva' correction
Microarray Microarray
12.5 years ago W. Evan Johnson ▴ 870
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1
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1.0k
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using beadarray or limma without spatial information
Microarray probe Microarray probe
updated 12.5 years ago by ★ 3.6k • written 12.5 years ago by ★ 13k
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1
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1.4k
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frmaTools library error :: makeVectorsAffyBatch() function
Microarray probe frma frmaTools Microarray probe frma frmaTools
updated 12.5 years ago by ▴ 830 • written 12.5 years ago by ▴ 70
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1
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1.6k
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2x3 factorial experiment
Microarray Microarray
updated 12.5 years ago by 68k • written 12.5 years ago by ▴ 10
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0
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969
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method or package to detect genes expressed in a specific tissue comparing to other tissues
RNASeq Microarray RNASeq Microarray
12.5 years ago shirley zhang ★ 1.0k
0
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1.6k
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How do I background correct an Illumina eset without using lumiB
Microarray probe limma PROcess convert beadarray lumi Microarray probe limma PROcess
12.5 years ago Gordon Smyth 53k
0
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1.3k
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problem with contrast.matrix and eBayes in limma
Microarray Microarray
12.5 years ago Gordon Smyth 53k
0
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4
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3.0k
views
Filtering is not recommended with LIMMA?
Microarray limma Microarray limma
updated 12.5 years ago by 53k • written 12.5 years ago by ▴ 150
0
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1
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1.7k
views
How do I background correct an Illumina eset without using lumiB?
Microarray probe PROcess convert beadarray lumi Microarray probe PROcess convert lumi
updated 12.5 years ago by ▴ 440 • written 12.5 years ago by ★ 13k
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4
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3.2k
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Average expression value from limma
Microarray Microarray
updated 12.5 years ago by 53k • written 12.5 years ago by ▴ 50
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10
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1.9k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray Coverage Microarray Coverage
12.5 years ago Thomas Girke ★ 1.7k
2,319 results • Page 16 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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