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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904
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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674
views
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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694
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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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660
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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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625
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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
638
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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937
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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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719
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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
17 months ago Sara ▴ 10
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4
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2.6k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 months ago by • 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 18 months ago by • 0
0
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1
reply
682
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
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8
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1.5k
views
Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
22 months ago YC • 0
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4
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1.0k
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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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826
views
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
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Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
24 months ago Yang Shi ▴ 10
3
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4
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1.7k
views
Quantile Normalization after rma or not?
limma Microarray oligo
24 months ago Yang Shi ▴ 10
2
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2
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809
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Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
hta20transcriptcluster.db Microarray oligo
24 months 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
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2
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781
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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
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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
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12
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1.5k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.1 years ago Adam • 0
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0
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625
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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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1.8k
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
replies
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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2.2k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 20 months ago by 50k • written 2.7 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 2.8 years ago by ▴ 10
3
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5
replies
1.6k
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
vote
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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1.3k
views
RUV4 for microarrays
RUV4 RUV Microarray
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
879
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
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2
replies
1.3k
views
How to quantile normalize arraystar lncRNA microarray data?
limma Microarray
3.1 years ago • updated 3.0 years ago a.deb • 0
3
votes
3
replies
1.3k
views
Weird MAplot with DEGs lying along the diagonals
limma Microarray AgilentChip MA-plot Normalization
3.2 years ago • updated 3.1 years ago FedeXander • 0
0
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2
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1.6k
views
WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
3.2 years ago jpwl2 • 0
6
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4
replies
1.2k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
1
vote
2
replies
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 • updated 3.2 years ago Dan ▴ 20
3
votes
9
replies
1.5k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.3 years ago • updated 3.2 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 • updated 3.5 years ago modarzi ▴ 10
1
vote
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
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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
3.6 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
2.1k
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
774
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
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1
reply
828
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
Recent ...
Replies
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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