Showing : Microarray • reset
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Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
1
vote
2
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914
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
13 months ago Abdul ▴ 20
2
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2
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680
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Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
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2
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710
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 13 months ago by 50k • written 13 months ago by • 0
2
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2
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671
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Question about avereps function of limma
avereps probes average limma Microarray
updated 14 months ago by 50k • written 14 months ago by ▴ 10
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0
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638
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
14 months ago jsharif • 0
0
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1
reply
648
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 15 months ago by 65k • written 15 months ago by • 0
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2
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952
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
16 months ago dqt • 0
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2
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728
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Celfiles not reading in
Microarray
written 16 months ago by • 0
6
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6
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1.4k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
18 months ago Sara ▴ 10
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4
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2.7k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 18 months ago by • 0
0
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17
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2.3k
views
Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 15 months ago by 50k • written 19 months ago by • 0
0
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1
reply
692
views
Compare different cell lines with tissues using limma
limma MicroarrayData Microarray Agilent
updated 22 months ago by 50k • written 22 months ago by • 0
0
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8
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1.5k
views
Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
23 months ago YC • 0
0
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4
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1.1k
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Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
23 months ago S • 0
1
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2
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837
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
1
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2
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1.1k
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
4
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10
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1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
2.0 years ago • updated 24 months ago Yang Shi ▴ 10
3
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4
replies
1.7k
views
Quantile Normalization after rma or not?
limma Microarray oligo
2.0 years ago Yang Shi ▴ 10
2
votes
2
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821
views
Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
2.0 years ago Yang Shi ▴ 10
2
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5
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1.8k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
2.0 years ago nhaus ▴ 30
0
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2
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796
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
2.0 years ago amir.rakhimov.b • 0
0
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2
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1.1k
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Time course experiment using limma
limma Multi-levelExperiments Microarray
2.1 years ago Wendy • 0
0
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12
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1.6k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.1 years ago Adam • 0
0
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0
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630
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Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
2.2 years ago emily • 0
2
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5
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1.9k
views
Adjust for base line gene expression in limma model
limma Microarray
updated 2.4 years ago by 50k • written 2.4 years ago by • 0
4
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6
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1.2k
views
RMA on different disease labels
rma background microarray normalization
updated 2.5 years ago by 65k • written 2.5 years ago by • 0
1
vote
1
reply
1.2k
views
Extracting a list of genes from the Gene Expression Omnibus with Geoquery.
Microarray GEOquery cancerdata MicroarrayData
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 50
5
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2
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2.3k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 21 months ago by 50k • written 2.8 years ago by ▴ 10
0
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1
reply
1.2k
views
Re-normalize microarray dataset in R
microarray quantile expression R Normalization
updated 2.8 years ago by ▴ 80 • written 2.9 years ago by ▴ 10
3
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5
replies
1.7k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
1
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1
reply
1.3k
views
How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
1
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2
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1.4k
views
RUV4 for microarrays
RUV4 RUV Microarray
3.1 years ago • updated 3.0 years ago Antonio • 0
0
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2
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2.1k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.1 years ago waiyin0923 • 0
0
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1
reply
883
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
1
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2
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1.3k
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
3.1 years ago a.deb • 0
3
votes
3
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1.4k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
3.2 years ago FedeXander • 0
0
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2
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1.7k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
3.2 years ago jpwl2 • 0
6
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4
replies
1.3k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.3 years ago snijesh ▴ 20
1
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2
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1.4k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
3.3 years ago Dan ▴ 20
3
votes
9
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1.5k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.3 years ago Daniel.Schnell • 0
0
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0
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1.3k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
3.6 years ago modarzi ▴ 10
1
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3
replies
2.4k
views
Annotating [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] file
microarray annotation affy
3.6 years ago kiera.lee ▴ 10
4
votes
7
replies
1.5k
views
Limma sample groups
microarray limma affy cancer
updated 3.6 years ago by 50k • written 3.6 years ago by • 0
0
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2
replies
1.2k
views
Regarding ArrayExpress package
microarray arrayexpress
updated 3.6 years ago by 65k • written 3.6 years ago by • 0
0
votes
2
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1.1k
views
What is the best way to do annotation of the transcript clusters and filter in HTA 2.0
HTA2.0 microarray affy r
3.7 years ago Marco_aurelio • 0
1
vote
6
replies
1.8k
views
can negative value microarray matrix data analysed by limma directly
limma microarray normalization
updated 9 months ago by 50k • written 3.7 years ago by ▴ 20
1
vote
6
replies
2.2k
views
TCGA: clinical data and expression data
microarray annotation cancer
updated 15 months ago by • 0 • written 3.7 years ago by • 0
3
votes
1
reply
777
views
Create a '.db' package for agilent
R agilent microarray
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 20
0
votes
1
reply
829
views
Problem for installing arrayQualityMetrics package?
R Microarray
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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