Showing : MicroarrayData • reset
1
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2
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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
5 weeks ago Mj.A. • 0
5
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7
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453
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DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
2
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6
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484
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
0
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3
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572
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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
5
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8
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1.5k
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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
1
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2
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756
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Error in getCdfInfo(object) :
MicroarrayData
12 months ago kobra • 0
0
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0
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617
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Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom Align MicroarrayData Alignment Microarray
14 months ago jsharif • 0
2
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1
reply
535
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Doubts about manipulation and annotation of microarray files deposited at GEO
MicroarrayData Annotation GEOdata
updated 15 months ago by 65k • written 15 months ago by • 0
0
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1
reply
632
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Micro Array GEO data analysis
GEOquery MicroarrayData Normalization Microarray NanoStringDiff
updated 15 months ago by 65k • written 15 months ago by • 0
0
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2
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926
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
16 months ago dqt • 0
2
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2
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566
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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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17
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2.3k
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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
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525
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Finding negative control in the array using R
R MicroarrayData
updated 20 months ago by 65k • written 20 months ago by • 0
0
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0
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506
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
20 months ago Fatemeh • 0
2
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2
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959
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
20 months ago Fatemeh • 0
1
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1
reply
632
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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
reply
676
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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
0
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8
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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
1
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2
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821
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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
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Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
0
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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 • updated 24 months ago amir.rakhimov.b • 0
0
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2
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758
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How to extract probe level intensity after rma() normalization
MicroarrayData AffymetrixChip
updated 2.0 years ago by 65k • written 2.0 years ago by • 0
0
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4
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921
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.1 years ago Haoran • 0
0
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1
reply
872
views
R CODE TO FIND AGGREGATE FOR DUPLICATES
aggregateBioVar DEGseq MicroarrayData
updated 2.4 years ago by 65k • written 2.4 years ago by • 0
0
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1
reply
692
views
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
1
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3
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1.1k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
0
votes
2
replies
647
views
Adj. P-value identical and high for all the genes
MicroarrayData
2.6 years ago Adriana • 0
1
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1
reply
1.2k
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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
3
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5
replies
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
1
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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
0
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2
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2.1k
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.0 years ago waiyin0923 • 0
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
6
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4
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1.2k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
3
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9
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1.5k
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limma analysis when only Cy5 was used
MicroarrayData limma Microarray
3.2 years ago Daniel.Schnell • 0
34 results • Page 1 of 1
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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 …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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