Showing : microarray • reset
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 29 days ago by ★ 4.7k • written 4 weeks ago by • 0
1
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8
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1.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
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5
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2.5k
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pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.0 years ago by ▴ 10
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4
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4.6k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 2.3 years ago by • 0
2
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2
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3.8k
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Biostatistician Position: UMass Medical School
Microarray Microarray
written 17.6 years ago by ▴ 190
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2
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 22 months ago by ▴ 70
1
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2
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1.4k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
22 months ago Abdul ▴ 20
2
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2
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961
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
22 months ago Abdul ▴ 20
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2
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1.0k
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 23 months ago by 52k • written 23 months ago by • 0
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6
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2.5k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 18 months ago by 52k • written 4.4 years ago by ▴ 20
2
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2
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1.0k
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Question about avereps function of limma
avereps probes average limma Microarray
updated 23 months ago by 52k • written 23 months ago by ▴ 10
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0
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893
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
24 months ago agamemnon • 0
0
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1
reply
900
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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2
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1.3k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.1 years ago dqt • 0
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2
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950
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Celfiles not reading in
Microarray
written 2.1 years ago by • 0
3
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2
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7.8k
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How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 2.2 years ago by ▴ 200 • written 7.2 years ago by • 0
6
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6
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1.8k
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
2.3 years ago • updated 2.2 years ago Sara ▴ 20
0
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17
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3.2k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.1 years ago by 52k • written 2.3 years ago by • 0
0
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1
reply
955
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
0
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8
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1.9k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
2.7 years ago YC • 0
2
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13
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5.2k
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Error in using r
microarray
updated 2.7 years ago by • 0 • written 8.4 years ago by • 0
0
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4
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1.3k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
2.7 years ago S • 0
1
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2
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1.1k
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
2.7 years ago Mikołaj Mierzejewski • 0
1
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2
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1.5k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
2.7 years ago Mikołaj Mierzejewski • 0
4
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10
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2.4k
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
2.8 years ago Yang Shi ▴ 10
3
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4
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2.3k
views
Quantile Normalization after rma or not?
limma Microarray oligo
2.8 years ago Yang Shi ▴ 10
2
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2
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1.1k
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
2.8 years ago Yang Shi ▴ 10
2
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5
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2.9k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.8 years ago nhaus ▴ 70
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2
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1.0k
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
2.8 years ago amir.rakhimov.b • 0
1
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2
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1.8k
views
Time course experiment using limma
limma Multi-levelExperiments Microarray
2.9 years ago • updated 2.8 years ago Wendy ▴ 10
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12
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2.0k
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Annotating featureData to an affymetrix Xcel microarray
Microarray
2.9 years ago Adam • 0
0
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0
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857
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
3.0 years ago emily • 0
1
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7
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9.2k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 2.9 years ago by • 0 • written 6.1 years ago by ▴ 10
2
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5
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2.3k
views
Adjust for base line gene expression in limma model
limma Microarray
updated 3.2 years ago by 52k • written 3.2 years ago by • 0
4
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6
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1.6k
views
RMA on different disease labels
rma background microarray normalization
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
1
vote
1
reply
1.5k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 50
5
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2
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3.1k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 2.5 years ago by 52k • written 3.5 years ago by ▴ 10
0
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1
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1.4k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 3.6 years ago by ▴ 80 • written 3.6 years ago by ▴ 10
3
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5
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2.1k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 3.6 years ago by 52k • written 3.7 years ago by • 0
1
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1
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1.8k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
1
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2
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1.9k
views
RUV4 for microarrays
RUV4 RUV Microarray
3.8 years ago Antonio • 0
0
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2
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2.4k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.8 years ago waiyin0923 • 0
0
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1
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1.1k
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.9 years ago by ★ 4.1k • written 3.9 years ago by • 0
1
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2
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1.6k
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
3.9 years ago • updated 3.8 years ago a.deb • 0
3
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3
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1.7k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4.0 years ago • updated 3.9 years ago FedeXandeR • 0
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2
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2.0k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.0 years ago jpwl2 • 0
8
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4
replies
1.6k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.0 years ago snijesh ▴ 200
1
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2
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1.7k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.0 years ago Dan ▴ 20
3
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9
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1.8k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
4.0 years ago Daniel.Schnell • 0
0
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1
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1.5k
views
Creating a model matrix for three age groups using two-colour arrays
Microarray BRAIN Microarray BRAIN
updated 4.1 years ago by 52k • written 16.3 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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