Showing : microarray • reset
2
votes
27
replies
3.0k
views
Applying NetAffx biological annotation to Affymetrix gene expression dataset
microarray annotation
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 10
3
votes
24
replies
4.2k
views
Problem in installing maEndToEnd package
microarray maEndToEnd
5.6 years ago • updated 5.5 years ago Jack • 0
6
votes
22
replies
4.7k
views
Oligo package: paCalls questions
microarray oligo
updated 9.8 years ago by ★ 3.9k • written 9.8 years ago by ▴ 20
0
votes
18
replies
7.2k
views
WGCNA error in network construction ?
microarray rnaseq
8.0 years ago m.azhar ▴ 10
0
votes
17
replies
3.4k
views
Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.1 years ago by 52k • written 2.4 years ago by • 0
0
votes
17
replies
3.1k
views
IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?
Microarray illuminaHumanv2 Microarray illuminaHumanv2
updated 11.7 years ago by ★ 4.2k • written 11.7 years ago by ▴ 190
0
votes
17
replies
3.2k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 11.9 years ago by ★ 13k • written 11.9 years ago by ▴ 330
0
votes
17
replies
3.1k
views
Defining Weights in marrayNorm.
Microarray Microarray
updated 21.6 years ago by ▴ 100 • written 21.6 years ago by ▴ 20
0
votes
16
replies
2.7k
views
liimma and Across Array Normalisation
Microarray Proteomics Microarray Proteomics
updated 11.1 years ago by 52k • written 11.1 years ago by ▴ 130
14
votes
16
replies
3.2k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 9.7 years ago by 68k • written 9.7 years ago by ▴ 10
0
votes
15
replies
3.1k
views
PreFiltering probe in microarray analysis
Microarray limma oligo Microarray limma oligo
updated 13.8 years ago by ▴ 220 • written 13.8 years ago by ▴ 30
8
votes
15
replies
10.0k
views
Design matrix for continuous independent variable in limma
limma microarray
9.2 years ago Linda Chaba ▴ 10
15
votes
14
replies
4.1k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 10.1 years ago by 21k • written 10.2 years ago by ▴ 340
4
votes
14
replies
6.1k
views
Including technical and biological replicates in Limma block analysis?
limma microarray block paired linear model
10.3 years ago vas ▴ 40
7
votes
13
replies
2.4k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 6.2 years ago by ★ 7.9k • written 6.2 years ago by ▴ 840
0
votes
13
replies
2.3k
views
Analysing DNA methylation microarrays in Bioconductor
Microarray Microarray
updated 14.7 years ago by ▴ 90 • written 14.7 years ago by ★ 1.3k
2
votes
13
replies
5.3k
views
Error in using r
microarray
updated 2.8 years ago by • 0 • written 8.4 years ago by • 0
8
votes
12
replies
4.6k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma microarray interaction model multiple factor design makeContrasts
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 840
0
votes
12
replies
2.5k
views
Quick start to linking GO terms and microarray data
Microarray GO affy PROcess goTools GOstats Microarray GO affy PROcess goTools GOstats
19.1 years ago michael watson IAH-C ★ 3.4k
1
vote
12
replies
2.5k
views
Illumina array analysis
Microarray Normalization limma Microarray Normalization limma
updated 13.4 years ago by ★ 3.6k • written 13.4 years ago by ▴ 310
1
vote
12
replies
5.4k
views
EdgeR: replicated pools, yes or not?
RNASeq Microarray edgeR RNASeq Microarray edgeR
updated 10.9 years ago by ★ 7.9k • written 10.9 years ago by ★ 13k
0
votes
12
replies
3.0k
views
gProcessed Signal normalization using cyclic loess
Microarray Normalization Microarray Normalization
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 580
0
votes
12
replies
3.9k
views
Understanding limma, fdr and topTable
Microarray GO limma Microarray GO limma
updated 16.7 years ago by ▴ 10 • written 16.7 years ago by ▴ 160
4
votes
12
replies
1.9k
views
Limma model for 4 factor (2*2*2*2) design to detect the factor specific effect and their interaction effect on gene expression
limma microarray
9.4 years ago baibing7713661 • 0
0
votes
12
replies
2.1k
views
Annotating featureData to an affymetrix Xcel microarray
Microarray
3.0 years ago • updated 2.9 years ago Adam • 0
0
votes
12
replies
6.8k
views
Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Microarray GO oligo AnnotationForge Microarray GO oligo AnnotationForge
12.1 years ago James W. MacDonald 68k
1
vote
12
replies
3.0k
views
avereps with probes mapping to multiple genes (Agilent dual color microarray)
limma avereps probe mapping microarray Agilent
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 30
0
votes
12
replies
2.7k
views
RNAseq machine learning classifier
RNASeq Microarray RNASeq Microarray
updated 11.7 years ago by ▴ 60 • written 11.7 years ago by ▴ 370
1
vote
12
replies
13k
views
Using limma for quantitative proteomics data
Microarray Proteomics limma Microarray Proteomics limma
12.8 years ago • updated 12.7 years ago Yong Li ▴ 80
6
votes
11
replies
2.6k
views
microarray data analsis with limma?
limma genepix microarray agilent microarrays
8.8 years ago Mehmet Ilyas Cosacak • 0
1
vote
11
replies
4.4k
views
oligo package requires the annotation package pd.ht.mg.430.pm - where is it?
oligo microarray annotation
updated 9.5 years ago by 68k • written 9.5 years ago by • 0
0
votes
11
replies
3.5k
views
Very low P-values in limma
miRNA Microarray Normalization GO vsn limma microRNA miRNA Microarray Normalization GO
updated 15.4 years ago by ★ 1.3k • written 15.4 years ago by 52k
3
votes
11
replies
3.1k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 6.6 years ago by 21k • written 6.6 years ago by ▴ 20
0
votes
11
replies
1.6k
views
error running makeProbePackage
Microarray probe Microarray probe
updated 12.9 years ago by 68k • written 12.9 years ago by ▴ 80
3
votes
11
replies
4.8k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 7.2 years ago by 21k • written 7.9 years ago by • 0
8
votes
11
replies
2.4k
views
Creating design matrix in LIMMA
limma microarray R
8.2 years ago sgblackpearl • 0
0
votes
11
replies
2.2k
views
...another question about using weights on microarray analysis
Microarray limma ASSIGN Microarray limma ASSIGN
16.1 years ago Erika Melissari ▴ 250
5
votes
11
replies
5.8k
views
Duplicate gene ID's returned from limma microarray analysis
limma microarray
updated 2.9 years ago by 52k • written 8.2 years ago by ▴ 80
0
votes
10
replies
2.7k
views
Microarray data analysis
Microarray Microarray
updated 11.0 years ago by 52k • written 11.0 years ago by ★ 13k
0
votes
10
replies
2.2k
views
AgiMicroRNA and Extra columns in Agilent Mouse miRNA Microarray Release 12.0 G4471A-021828.
miRNA Microarray Cancer microRNA miRNA Microarray Cancer microRNA
14.8 years ago Neel Aluru ▴ 460
0
votes
10
replies
18k
views
Fine tuning heatmap.2 graphics
Microarray Microarray
updated 19.0 years ago by ▴ 290 • written 19.0 years ago by ▴ 70
0
votes
10
replies
3.1k
views
ANCOVA microarray time-course continuous & categorical variables / Limma extensions
RNASeq Microarray limma RNASeq Microarray limma
updated 11.4 years ago by 52k • written 11.4 years ago by ▴ 370
3
votes
10
replies
2.4k
views
Still need help identifying a good workflow for finding DEG in hugene 2.0 st
microarray hugene20 limma oligo
updated 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
8
votes
10
replies
5.5k
views
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
limma topTable confidence interval effect size microarray
updated 9.0 years ago by 52k • written 9.0 years ago by ▴ 80
0
votes
10
replies
2.2k
views
exonmap RMA function
Microarray Cancer affyPLM exonmap Microarray Cancer affyPLM exonmap
updated 17.2 years ago by ▴ 250 • written 17.2 years ago by 25k
0
votes
10
replies
1.7k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Microarray Coverage Microarray Coverage
11.8 years ago Thomas Girke ★ 1.7k
0
votes
10
replies
3.4k
views
PAIR files -- feature set table
Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism
updated 11.8 years ago by ★ 4.3k • written 11.8 years ago by ★ 13k
0
votes
10
replies
2.1k
views
Read single channel GenePix in limma [was: Analyze miRNA experiment in Bioconductor]
miRNA Microarray Normalization GO limma miRNA Microarray Normalization GO limma
updated 16.9 years ago by ★ 1.3k • written 16.9 years ago by 52k
0
votes
10
replies
3.2k
views
RMA/QuantileNormalization results difference between oligo and aroma.affymetrix for Hugene
Microarray Normalization cdf oligo DTA Microarray Normalization cdf oligo DTA
updated 15.1 years ago by ★ 4.3k • written 15.1 years ago by ▴ 110
0
votes
10
replies
2.6k
views
Retrieve Entrez IDs for enriched GO terms
Microarray Annotation GO limma GOstats biomaRt Microarray Annotation GO limma GOstats
updated 15.5 years ago by ★ 2.0k • written 15.5 years ago by ▴ 90
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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