Showing : MicroarrayData • reset
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Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 14 months ago by 50k • written 18 months ago by • 0
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.0 years ago waiyin0923 • 0
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2
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1.6k
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WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
3.2 years ago jpwl2 • 0
3
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5
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1.6k
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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
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9
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1.4k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.2 years ago Daniel.Schnell • 0
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1.4k
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Finding differentially expressed genes in a prospective cohort study
limma MicroarrayData Microarray
22 months ago YC • 0
5
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8
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Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
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1.3k
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How do I adjust for other factors in Limma differential expression analysis?
limma Microarray MicroarrayData arrays
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
6
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4
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1.2k
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
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1
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1.1k
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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
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3
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1.1k
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Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 2.6 years ago by 65k • written 2.6 years ago by • 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
22 months ago Mikołaj Mierzejewski • 0
2
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2
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928
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
20 months ago Fatemeh • 0
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2
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900
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
15 months ago dqt • 0
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4
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897
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.1 years ago Haoran • 0
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1
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858
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R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 2.4 years ago by 65k • written 2.4 years ago by • 0
1
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2
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802
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
22 months ago Mikołaj Mierzejewski • 0
0
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2
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763
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Identifying multiple mappings with pd.clariom.d.human
clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human
23 months ago amir.rakhimov.b • 0
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2
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737
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 23 months ago by 65k • written 23 months ago by • 0
1
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2
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733
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Error in getCdfInfo(object) :
MicroarrayData
12 months ago kobra • 0
0
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1
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682
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Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
.gpr raw Agilent MicroarrayData import
updated 2.5 years ago by 50k • written 2.5 years ago by • 0
0
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1
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655
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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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2
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634
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Adj. P-value identical and high for all the genes
MicroarrayData
2.6 years ago Adriana • 0
1
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1
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623
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IS DGE possible with normalized microarray expression data and Limma ?
limma MicroarrayData
updated 21 months ago by 65k • written 21 months ago by • 0
0
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1
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616
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 14 months ago by 65k • written 14 months ago by • 0
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0
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600
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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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3
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546
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Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 8 months ago by 50k • written 8 months ago by • 0
2
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2
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545
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2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip MicroarrayData Anova
18 months ago evan.j.williams ▴ 10
0
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1
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515
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Finding negative control in the array using R
R MicroarrayData
updated 19 months ago by 65k • written 19 months ago by • 0
2
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1
reply
514
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 14 months ago by 65k • written 14 months ago by • 0
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0
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493
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
20 months ago Fatemeh • 0
2
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6
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437
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
6 weeks ago • updated 25 days ago Lily Cheang ▴ 10
5
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7
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419
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DEG Filtering
MicroarrayData limma Genefiltering
updated 23 days ago by 50k • written 4 weeks ago by • 0
1
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2
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208
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Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function rma_function ExpressionSet MicroarrayData affy
24 days ago Mj.A. • 0
34 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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