Showing : MicroarrayData • reset
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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
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
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
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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
5
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7
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449
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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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481
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limma: vooma mean-variance trend and data filtration
MicroarrayData limma
8 weeks ago • updated 5 weeks ago Lily Cheang ▴ 10
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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4
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919
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getProbeInfo and exprs return two different dimensions
CELfile MicroarrayData AffymetrixChip
2.1 years ago Haoran • 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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3
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570
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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
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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
2
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2
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957
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the difference between getGEO and getGEOSuppFiles
MicroarrayData
20 months ago Fatemeh • 0
0
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2
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755
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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
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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
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2
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How to exclude outlier (Microarray ) from PCA in R
OutlierD pcaMethods MicroarrayData Microarray
3.0 years ago waiyin0923 • 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
1
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2
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227
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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
1
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2
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820
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 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
0
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2
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647
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Adj. P-value identical and high for all the genes
MicroarrayData
2.6 years ago Adriana • 0
0
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2
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925
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Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
16 months ago • updated 15 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
1
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2
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755
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Error in getCdfInfo(object) :
MicroarrayData
12 months ago kobra • 0
0
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1
reply
870
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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
0
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1
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524
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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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1
reply
631
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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
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
1
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1
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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 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
1
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1
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631
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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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692
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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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675
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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
2
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1
reply
533
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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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614
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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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0
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505
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Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
20 months ago Fatemeh • 0
34 results • Page 1 of 1
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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