Showing : microarray • reset
5
votes
7
replies
2.8k
views
Analyse Microarray Data - AVG_Signal
limma microarray
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
0
votes
3
replies
1.4k
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA combat r microarray covariates
updated 6.1 years ago by 25k • written 6.1 years ago by • 0
0
votes
1
reply
639
views
Annotation Dbi replaced by utils
microarray annotation
6.1 years ago ekl • 0
1
vote
2
replies
1.6k
views
What should I do with the package:org.Hs.eg.db?
microarray affy
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 10
1
vote
2
replies
779
views
Error in write.fit step using limma package for microarray analysis
limma microarray
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
0
votes
3
replies
745
views
Help with Affymetrix Human Genome U95A 2.0
microarray
6.2 years ago pablo.giraudi • 0
3
votes
24
replies
4.9k
views
Problem in installing maEndToEnd package
microarray maEndToEnd
6.3 years ago • updated 6.2 years ago Jack • 0
1
vote
2
replies
2.5k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
3
votes
4
replies
1.4k
views
How to check whether experimental covariates are confounded with our group of interest?
covariates microarray
6.2 years ago english.server ▴ 20
0
votes
3
replies
1.9k
views
Subsetting a data frame generated by topTable() {limma}
limma toptable microarray
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 30
6
votes
4
replies
4.9k
views
AnnotationData Packages for Agilent microarrays
microarray annotation limma .db Agilent
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 30
0
votes
5
replies
1.7k
views
Does anyone have experience using the massiR package?
massiR microarray R probe
6.2 years ago Steve Lowe ▴ 30
0
votes
0
replies
866
views
massiR Extracting and Plotting Y Chr Probe Data
probe microarray
6.2 years ago Steve Lowe ▴ 30
0
votes
0
replies
1.1k
views
Different versions of r/affy combination may lead to differences in rma normalization results
microarray affy rma normalization affy package
6.3 years ago yshuang • 0
1
vote
2
replies
2.9k
views
CDF not found
Affy microarray
updated 6.3 years ago by ★ 4.1k • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Determining survival correlation among probes
annotation probe microarray
6.3 years ago sbrackett007 • 0
2
votes
1
reply
1.5k
views
Limma Design matrix for time series+treatment+batch effect
limma factorial design matrix microarray
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
0
votes
0
replies
1.1k
views
Any recommended workflow for incrementally selecting top ranked genes by using mRMR feature selection?
microarray gene-filtering mRMR parallel-processing bioconductor-package
6.4 years ago • updated 6.3 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
1.0k
views
Microarray Data Analysis CDF Problem
microarray normalization
updated 6.4 years ago by ★ 4.1k • written 6.4 years ago by • 0
0
votes
2
replies
1.5k
views
R: rma() function error
rma normalization microarray
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
0
votes
1
reply
633
views
Non-parametrical Differential Expression Analysis in Microarrays
microarray
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
2
votes
3
replies
1.6k
views
How can I overcome the error of "No residual degrees of freedom in linear model fits"?
limma microarray error
updated 6.4 years ago by ★ 1.6k • written 6.4 years ago by ▴ 80
0
votes
1
reply
587
views
Annmap database accession problem
software error microarray
6.4 years ago kubracelikbas4 • 0
1
vote
2
replies
1.5k
views
MINFI Data merging and Normalization
microarray
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
9
votes
10
replies
3.0k
views
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
limma microarray genefilter deseq2
6.4 years ago Jurat Shahidin ▴ 80
0
votes
0
replies
1.0k
views
Fold Change Calculation in edge package
edge microarray limma affy
6.4 years ago soumyab.g ▴ 10
6
votes
8
replies
2.5k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
6.5 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
1.3k
views
"hgu133plus2db" package not working in R
microarray affy annotation
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
3
replies
1.3k
views
How to find number of patients (percentage of given population) having high expression of gene A in given microarray data ?
microarray r clustering high expressed genes
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
6
replies
2.8k
views
Save ExpressionSet to csv file with columns and rows headers
microarray genefilter
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
2
votes
1
reply
2.1k
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
6.5 years ago epibio ▴ 10
2
votes
2
replies
756
views
How to get the final value of the after an automatic method in SAM
microarray SAM
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
0
votes
4
replies
1.8k
views
Creating an Expression Set from a csv file or EXCEL file
microarray
updated 6.5 years ago by ★ 1.4k • written 6.5 years ago by ▴ 10
1
vote
1
reply
920
views
export the significant results from EDGE
microarray edge
6.5 years ago xgt1986627 ▴ 10
0
votes
0
replies
848
views
static experiment in EDGE
microarray edge
6.5 years ago xgt1986627 ▴ 10
0
votes
0
replies
951
views
Warning: Error in impute.knn in SAM
software error microarray
6.5 years ago xgt1986627 ▴ 10
0
votes
7
replies
2.8k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 6.6 years ago by ★ 4.1k • written 6.6 years ago by • 0
0
votes
7
replies
1.9k
views
How to read Illumina data used in the MACQ project (GSE5350)
microarray normalization Illumina data MACQ project gene expression
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
3
votes
9
replies
3.0k
views
design and contrast matrix for limma (time course with 2 different genotypes)
limma microarray
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 10
1
vote
2
replies
671
views
Heatmap of subset of genes from data matrix file
microarray
6.6 years ago andrea.hain • 0
0
votes
1
reply
566
views
Downloading Gene2pathway for Mac
gene2pathway microarray
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
2
votes
2
replies
1.1k
views
limma: include samples from multiple treatments?
limma microarray
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
1
vote
3
replies
545
views
Hello All can any one please help?
microarray bioconductor R
6.6 years ago sumode • 0
0
votes
6
replies
14k
views
Package version of Bioconductor cannot be unloaded, Error in unloadNamespace(package),help!!
microarray software error hgu133plus2.db
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
votes
3
replies
1.8k
views
How to regress phenotype ~ gene + covars in limma?
limma gene expression microarray R
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
1
vote
2
replies
1.9k
views
How do I creat an expressionset if there is no GDS listed on the GEO database?
limma microarray GEOquery
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
2
votes
0
replies
1.7k
views
Limma - decideTests - separate/nestedF questions
Microarray limma
18.6 years ago • updated 6.6 years ago Gordon Smyth 53k
0
votes
0
replies
3.3k
views
Clusterprofiler error, No gene can be mapped
microarray clusterprofiler
6.7 years ago rm1238 • 0
0
votes
0
replies
520
views
Co expression analysis of rice affymetrix data
coexpression analysis microarray
6.7 years ago pratikshasharma47 • 0
0
votes
3
replies
1.8k
views
usage of topGO after limma
limma topGO microarray
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
2,319 results • Page 3 of 47
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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