Showing : microarray • reset
2
votes
2
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1.1k
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 4 days ago by • 0 • written 7.9 years ago by • 0
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 12 days ago by • 0 • written 7.7 years ago by ▴ 30
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
2
votes
2
replies
2.4k
views
Biostatistician Position: UMass Medical School
Microarray Microarray
written 16.8 years ago by ▴ 190
1
vote
4
replies
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
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 7 months ago by 50k • written 5.2 years ago by • 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
0
votes
2
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1.4k
views
Calculation of t-tests for factorial design
Microarray limma Microarray limma
written 13.7 years ago by ▴ 80
0
votes
2
replies
706
views
Probe off-target prediction: Identifying short sequence matches - potentially with mismatches & indels - in a transcriptome
Microarray Alignment Biostrings
written 12 months ago by ▴ 70
0
votes
7
replies
1.4k
views
A question about Limma
PROcess Microarray limma
19.3 years ago • updated 11 months ago Gordon Smyth 50k
1
vote
2
replies
899
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
votes
2
replies
665
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
13 months ago Abdul ▴ 20
0
votes
2
replies
686
views
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
votes
2
replies
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
0
votes
0
replies
617
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
14 months ago jsharif • 0
7
votes
1
reply
15k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 14 months ago by • 0 • written 10.0 years ago by ▴ 40
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
0
votes
17
replies
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
votes
1
reply
632
views
Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 15 months ago by 65k • written 15 months ago by • 0
0
votes
2
replies
927
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
16 months ago dqt • 0
0
votes
2
replies
715
views
Celfiles not reading in
Microarray
written 16 months ago by • 0
2
votes
6
replies
3.6k
views
Convert Chromosome postions to hgnc_symbol using R
microarray
updated 16 months ago by • 0 • written 4.4 years ago by • 0
1
vote
2
replies
6.2k
views
How to convert Illumina HT_12_v4 annotation
convert R annotation microarray illumina human ht-12 v4
updated 17 months ago by ▴ 20 • written 6.4 years ago by • 0
6
votes
6
replies
1.4k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
17 months ago Sara ▴ 10
5
votes
2
replies
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
votes
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
votes
8
replies
1.4k
views
Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
22 months ago YC • 0
2
votes
13
replies
4.5k
views
Error in using r
microarray
updated 23 months ago by • 0 • written 7.5 years ago by • 0
0
votes
4
replies
1.0k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
23 months ago S • 0
1
vote
2
replies
822
views
Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
4
votes
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
votes
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
23 months ago Yang Shi ▴ 10
2
votes
5
replies
1.8k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
24 months ago nhaus ▴ 30
0
votes
2
replies
778
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
2.0 years ago amir.rakhimov.b • 0
5
votes
11
replies
4.9k
views
Duplicate gene ID's returned from limma microarray analysis
limma microarray
updated 2.0 years ago by 50k • written 7.3 years ago by ▴ 70
0
votes
2
replies
1.1k
views
Time course experiment using limma
limma Multi-levelExperiments Microarray
2.1 years ago • updated 2.0 years ago Wendy • 0
0
votes
12
replies
1.5k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.1 years ago Adam • 0
1
vote
7
replies
7.6k
views
Oligo RMA normalization : ERROR; return code from pthread_create() is 22
microarray normalization oligo HTA
updated 2.1 years ago by • 0 • written 5.3 years ago by ▴ 10
0
votes
0
replies
622
views
Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
2.2 years ago emily • 0
2
votes
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
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.7 years ago by • 0 • written 13.5 years ago by ▴ 120
0
votes
1
reply
1.1k
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
3
votes
6
replies
4.4k
views
Affymetrix miRNA 4.0 Normalization and Analysis
R Limma microarray miRNA
updated 3.0 years ago by ▴ 10 • written 8.2 years ago by ▴ 90
1
vote
2
replies
1.3k
views
RUV4 for microarrays
RUV4 RUV Microarray
3.0 years ago Antonio • 0
50 results • Page 1 of 1
Recent ...
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Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result by ATpoint ★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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