Showing : microarray • reset
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 4 months ago by 53k • written 16.8 years ago by ▴ 10
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2
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659
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affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 8 months ago by 68k • written 8 months ago by • 0
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1
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570
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
1
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8
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2.5k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 12 months ago by • 0
1
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5
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2.8k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 10.8 years ago by ▴ 10
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4
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6.0k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.0 years ago by • 0
2
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2
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4.1k
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Biostatistician Position: UMass Medical School
Microarray Microarray
written 18.4 years ago by ▴ 190
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1.3k
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 2.6 years ago by ▴ 70
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2
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1.7k
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Filter by expression and keep probes in limma
R filter limma Normalization Microarray
2.6 years ago Abdul ▴ 20
2
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2
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1.2k
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
2.6 years ago Abdul ▴ 20
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2
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1.3k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
1
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6
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3.0k
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can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 2.3 years ago by 53k • written 5.2 years ago by ▴ 20
2
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2
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1.4k
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Question about avereps function of limma
avereps probes average limma Microarray
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
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0
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1.1k
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
2.8 years ago agamemnon • 0
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1
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1.1k
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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2
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1.7k
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.9 years ago dqt • 0
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2
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1.1k
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Celfiles not reading in
Microarray
written 2.9 years ago by • 0
3
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2
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8.9k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 3.0 years ago by ▴ 200 • written 8.0 years ago by • 0
6
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6
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2.2k
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Too many differentially expressed miRNA with limma
limma miRNA Microarray
3.0 years ago Sara ▴ 20
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17
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4.2k
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.8 years ago by 53k • written 3.1 years ago by • 0
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1
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1.2k
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Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
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2.2k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
3.4 years ago YC • 0
2
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13
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5.7k
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Error in using r
microarray
updated 3.5 years ago by • 0 • written 9.1 years ago by • 0
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4
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1.6k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
3.5 years ago S • 0
1
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2
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1.3k
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
3.5 years ago Mikołaj Mierzejewski • 0
1
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2
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1.9k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
3.5 years ago Mikołaj Mierzejewski • 0
4
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10
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3.0k
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
3.5 years ago Yang Shi ▴ 10
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4
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2.7k
views
Quantile Normalization after rma or not?
limma Microarray oligo
3.5 years ago Yang Shi ▴ 10
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2
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1.3k
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Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
3.5 years ago Yang Shi ▴ 10
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5
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3.8k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
3.6 years ago nhaus ▴ 70
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1.2k
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
3.6 years ago amir.rakhimov.b • 0
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2.2k
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Time course experiment using limma
limma Multi-levelExperiments Microarray
3.6 years ago Wendy ▴ 10
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12
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2.4k
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Annotating featureData to an affymetrix Xcel microarray
Microarray
3.6 years ago Adam • 0
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1.0k
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
3.7 years ago emily • 0
1
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7
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10k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 3.7 years ago by • 0 • written 6.8 years ago by ▴ 10
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5
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2.7k
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Adjust for base line gene expression in limma model
limma Microarray
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
4
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6
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2.0k
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RMA on different disease labels
rma background microarray normalization
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
1
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1
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1.8k
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Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 50
5
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3.5k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 3.3 years ago by 53k • written 4.3 years ago by ▴ 10
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1
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1.6k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 4.4 years ago by ▴ 90 • written 4.4 years ago by ▴ 10
3
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5
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2.5k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 4.4 years ago by 53k • written 4.5 years ago by • 0
1
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1
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2.1k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
1
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2
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2.2k
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RUV4 for microarrays
RUV4 RUV Microarray
4.6 years ago Antonio • 0
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2
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2.8k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
4.6 years ago waiyin0923 • 0
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1
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1.3k
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Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 4.6 years ago by ★ 4.1k • written 4.6 years ago by • 0
1
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2
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2.2k
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How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
4.7 years ago • updated 4.6 years ago a.deb • 0
3
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3
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1.9k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
4.7 years ago FedeXandeR • 0
0
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2
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2.4k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.8 years ago jpwl2 • 0
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4
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1.9k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.8 years ago snijesh ▴ 200
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2
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1.9k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.8 years ago Dan ▴ 20
2,319 results • Page 1 of 47
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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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