Showing : microarray • reset
0
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4
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7.9k
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Limma Volcano Plot Highlight Top Genes by Color
limma microarray volcanoplot color
updated 7.1 years ago by 53k • written 7.1 years ago by • 0
0
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2
replies
1.2k
views
Need Guidance Regarding the Results of Microarray Pipeline
microarray maEndtoEnd
updated 7.1 years ago by 53k • written 7.2 years ago by • 0
2
votes
6
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3.2k
views
extracting the genes associated with the groups or samples in pheatmap.
R microarray
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
3
votes
1
reply
2.2k
views
difference between pd.hugene.2.1.st and hugene21sttranscriptcluster.db
annotation microarray bioconductor pd.hugene.2.1.st hugene21sttranscriptcluster.db
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
1
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2
replies
1.5k
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
0
votes
0
replies
961
views
Computing se.exprs in R for an Expressionset?
microarray Expressionset se.exprs
7.2 years ago payam_delfani1980 • 0
3
votes
1
reply
1.6k
views
DE genes comparison of different treatments from microarray and RNAseq data
microarray deseq2 limma edgeR
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
3
votes
11
replies
3.6k
views
Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 7.3 years ago by 21k • written 7.3 years ago by ▴ 20
1
vote
2
replies
1.9k
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 10
1
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3
replies
1.3k
views
Filtering the expression values of a gene from GEO
GEO microarray
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 20
0
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0
replies
1.1k
views
Assessing goodness of fit of a limma model fitted to microarray data
limma microarray goodness of fit
7.3 years ago rubi ▴ 110
0
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1
reply
1.9k
views
Finding/Understanding Affy 6.0 Annotation File
affy affymetrix microarray SNP
7.3 years ago CantExitVIM ▴ 10
3
votes
4
replies
1.1k
views
Compare in cont.matrix part
microarray R
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 10
1
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3
replies
1.4k
views
remove NAs values from gset
microarray R
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 10
3
votes
8
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2.0k
views
Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
limma microarray design matrix twochannel
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 110
7
votes
1
reply
17k
views
ERROR: No residual degrees of freedom in linear model fits
Microarray
updated 2.8 years ago by • 0 • written 11.6 years ago by ▴ 40
0
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4
replies
2.4k
views
Simple differential expression analysis for 2 groups
differential gene expression agilent microarrays microarray DEA Limma
7.3 years ago christiangriffioen • 0
2
votes
3
replies
1.0k
views
affy() can not read MoGene2_0-st.CEL file
microarray
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
0
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4
replies
2.0k
views
Guidance to handle .CEL file in R
R .cel fiels microarray mouse4302
7.4 years ago aacharya • 0
1
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4
replies
2.1k
views
venDiagram after limma showing more genes after specifying up or down regulated specifically
venn diagram venndiagram limma microarray differential expression
updated 7.4 years ago by 68k • written 7.4 years ago by ▴ 60
2
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2
replies
3.0k
views
Error in log2(exprs(eSet)) : non-numeric argument to mathematical function
microarray biobase
7.4 years ago charlesgwellem ▴ 20
1
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2
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2.2k
views
Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from …
limma microarray agilent microarrays GEO
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
0
votes
1
reply
799
views
limma tutorial for microarray data analysis
microarray
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
3
votes
4
replies
1.7k
views
Agilent Single-Channel Data: Questions about model statement and model building.
limma agilent microarray covariates
updated 7.6 years ago by 53k • written 7.6 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm gsa microarray illumina
written 7.6 years ago by • 0
3
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6
replies
2.0k
views
Design/contrast matrix for Multivariate experimental design in limma
microarray limma design and contrast matrix
updated 7.6 years ago by 53k • written 7.6 years ago by ▴ 30
3
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2
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1.8k
views
How to find the degree of freedom, effect size and the variance of effect size for each contrast
limma microarray
updated 7.6 years ago by • 0 • written 7.7 years ago by ▴ 20
1
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2
replies
1.4k
views
affymetrix miRNA microarray analysis, (package mirna30cdf)
microarray affy
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 20
0
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0
replies
1.4k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
7.7 years ago aagata.szymanek • 0
0
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2
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3.8k
views
Can't Use "getGEO" Command Function in R Program
microarray software error bioconductor affy R
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
0
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0
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1.6k
views
Probe annotations for ABI Human Genome Survey V2 microarray using Oracle
annotation probe microarray abi human genome survey v2 Oracle
7.7 years ago judemtaylor • 0
1
vote
4
replies
1.9k
views
Upregulation and Downregulation of Gene Ontology terms
microarray david differential gene expression GO
7.7 years ago seendey16 • 0
0
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0
replies
1.3k
views
Error in building expression set for ArrayExpress
microarray expressionset arrayexpress bioconductor r
7.7 years ago rf • 0
0
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0
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671
views
plotMA is not centered around zero for logFC
microarray differential gene expression
7.7 years ago twentestat • 0
1
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3
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1.7k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.7 years ago cherlyn.t • 0
0
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1
reply
1.6k
views
Reading in .gpr files
microarray
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 20
0
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5
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2.0k
views
How to normalize mouse gene 1.0st arry using frma?
microarray frma
updated 7.7 years ago by • 0 • written 8.5 years ago by • 0
0
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0
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2.2k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2 hierarchical clustering microarray RNA seq DEG
7.8 years ago lawarde.ankita1 ▴ 30
1
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1
reply
923
views
Fold Change and LogFC
limma microarray
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
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3
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2.5k
views
File format for single channel analysis of Agilent microarray data with Limma?
Microarray Microarray
updated 7.8 years ago by 53k • written 13.5 years ago by ★ 13k
7
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8
replies
2.9k
views
Microarray analysis using RMA method using affy, limma
microarray annotation aureus affy
7.8 years ago neranjan007 • 0
0
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1
reply
1.8k
views
Analysing microarray raw data: GSEXXXX_non-normalized.txt
lumi microarray GSE
updated 7.8 years ago by 53k • written 7.8 years ago by • 0
1
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9
replies
3.8k
views
Removing batch effects from microarray data based on only a subset of samples
limma removebatcheffect() ComBat microarray
7.8 years ago jaro.slamecka ▴ 140
0
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1
reply
945
views
ExpressionSet annotation with custom annotation file
annotation microarray R
7.8 years ago genesignature • 0
3
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11
replies
5.4k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 7.8 years ago by 21k • written 8.6 years ago by • 0
1
vote
1
reply
1.5k
views
Unknown gene names in pd.clariom.d.human annotation package
microarray pd.clariom.d.human
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 10
0
votes
2
replies
1.5k
views
RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
RUVnormalize limma corrected expression matrix microarray
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by • 0
1
vote
3
replies
1.7k
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 70
0
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0
replies
1.6k
views
Two questions about pathifier package
pathways statistics microarray
7.9 years ago arronar • 0
1
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3
replies
5.3k
views
How to select top 10% highly variable genes in microarray data?
r microarray snp6.0 oligo
updated 7.9 years ago by ▴ 360 • written 7.9 years ago by ▴ 120
2,319 results • Page 5 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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