Showing : microarray • reset
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 7 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
1.7k
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
replies
1.4k
views
Calculation of t-tests for factorial design
Microarray limma Microarray limma
written 13.6 years ago by ▴ 80
0
votes
2
replies
692
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
885
views
Filter by expression and keep probes in limma
R filter limma Normalization Microarray
12 months ago Abdul ▴ 20
2
votes
2
replies
658
views
Question about transforming log expression values to antilog values in limma
IlluminaChip limma AffymetrixChip Normalization Microarray
12 months ago Abdul ▴ 20
0
votes
2
replies
680
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
650
views
Question about avereps function of limma
avereps probes average limma Microarray
updated 13 months ago by 50k • written 13 months ago by ▴ 10
0
votes
0
replies
610
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 14 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
627
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
921
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
15 months ago dqt • 0
0
votes
2
replies
710
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 16 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
671
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 22 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
815
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
799
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
771
views
Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
24 months 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
2.0 years ago Wendy • 0
0
votes
12
replies
1.5k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
2.1 years ago • updated 2.0 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
618
views
Error in svd(X) when using edge lrt (or odp) function.
edge Microarray longitudinal
2.1 years ago emily • 0
2
votes
5
replies
1.8k
views
Adjust for base line gene expression in limma model
limma Microarray
updated 2.3 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
1.1k
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
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
50 results • Page 1 of 1
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Answer: Version 3.15 S4Vectors packages are missing by shepherl 3.8k
It is missing because that package did not have any updates in the release except for the initial version. The archive directory holds prev…
Comment: putting my own expression data in deseq2 by ATpoint ★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha by SSSJec • 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score? by Gordon Smyth 50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by Chris • 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
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Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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