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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899
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
votes
2
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667
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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686
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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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656
views
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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618
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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
634
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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928
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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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715
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Celfiles not reading in
Microarray
written 16 months ago by • 0
6
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6
replies
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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2.5k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 17 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 18 months ago by • 0
0
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1
reply
677
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
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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823
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
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
4
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10
replies
1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219 Microarray oligo AffymetrixChip
23 months ago Yang Shi ▴ 10
3
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4
replies
1.6k
views
Quantile Normalization after rma or not?
limma Microarray oligo
23 months ago Yang Shi ▴ 10
2
votes
2
replies
804
views
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
24 months ago nhaus ▴ 30
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2
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778
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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
views
Time course experiment using limma
limma Multi-levelExperiments Microarray
2.1 years ago • updated 2.0 years ago Wendy • 0
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
0
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0
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624
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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
replies
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
votes
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 2.6 years ago by 65k • written 2.6 years ago by ▴ 50
5
votes
2
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2.2k
views
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
votes
5
replies
1.6k
views
Use of arrayWeights with two treatment groups
Microarray arrays limma MicroarrayData
updated 2.8 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
replies
1.3k
views
RUV4 for microarrays
RUV4 RUV Microarray
3.0 years ago Antonio • 0
0
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2
replies
2.1k
views
How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.0 years ago waiyin0923 • 0
0
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1
reply
875
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
vote
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
votes
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
3.2 years ago Dan ▴ 20
3
votes
9
replies
1.5k
views
limma analysis when only Cy5 was used
MicroarrayData limma Microarray
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
3.5 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
votes
2
replies
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 8 months ago by 50k • written 3.6 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 3.6 years ago by • 0
3
votes
1
reply
773
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
826
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: fgsea significant result by Chris • 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons by Michael Love 41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Votes
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
package goseq seems to be not available on the latest version of R
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