Showing : microarray • reset
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Why the threshold rank invariant normalization(Invariant set normalization) needs to be *10?
microarray normalization
7.9 years ago dasiav7 • 0
4
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2
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1.9k
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How to check if the microarray data is from codelink
codelink microarray
updated 7.9 years ago by 21k • written 7.9 years ago by ▴ 260
2
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8
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2.6k
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Transcript-level SCAN.UPC preprocessing for Affymetrix HTA 2.0 arrays
microarray scan.upc hta2.0
updated 7.9 years ago by ▴ 600 • written 7.9 years ago by • 0
0
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2
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1.4k
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Does bioconductor now has microarray cross-platform merging and normalization methods?
software error microarray
updated 7.9 years ago by ★ 13k • written 7.9 years ago by • 0
2
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2
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1.5k
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How to add more columns to ReportingTools output?
reportingtools microarray annotation differential expression differential analysis
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
0
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1
reply
1.8k
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Error in Expression File Creator
microarray software error affymetrix microarrays
8.0 years ago parin.kamseng • 0
0
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2
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1.9k
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R packages for differential expression analysis of raw data from arraystar microarrays
microarray lncrna microrna mrna raw data
updated 8.0 years ago by ★ 1.1k • written 8.0 years ago by • 0
0
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1
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1.0k
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R version and packages problems
affy bioconductor microarray
8.0 years ago amaalkalds • 0
0
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2
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2.6k
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Differential expression between multiple groups
multiple groups differential gene expression microarray
8.0 years ago A ▴ 60
1
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6
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4.2k
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Two-way anova 2x2 design with limma
limma microarray differential expression
8.0 years ago damoros • 0
1
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2
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1.9k
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Rstudio session aborts when using read.celfiles()
oligo package Rstudio fatal error microarray CEL
8.0 years ago biostR ▴ 10
2
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2
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1.8k
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how to obtain differentially expressed genes from a GSE serie
microarray GSE
8.0 years ago Salvo88 ▴ 20
1
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1
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1.9k
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Error in Rnbeads:Error in logger.error(em) : Could not create file. cannot popen '/usr/bin/which 'gs' 2>/dev/null', probable reason 'Cannot alloca…
R bioconductor rnbeads microarray illimina 450k methylation
8.0 years ago preethibagopi28 ▴ 10
1
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2
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1.9k
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Subsetting GSE data with information from two different slots
GSE subsetting microarray
updated 8.1 years ago by ★ 1.1k • written 8.1 years ago by ▴ 60
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1
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1.0k
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Diferential expresion analysis between different microarray platforms
microarray platforms
8.1 years ago n.lu • 0
3
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2
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1.5k
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How is microarray normalization done in PIANO?
piano microarray
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
0
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1
reply
1.9k
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Downloading Twochannel microarray data from ArrayExpress
arrayexpress twochannel microarray
8.1 years ago Andy91 ▴ 60
0
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0
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1.5k
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Need help determine optimal argument value on a rbsurv model
rbsurv microarray survival
8.1 years ago JackieMe • 0
17
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8
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12k
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remove microarray batch effects using Limma
Microarray
updated 17 months ago by 53k • written 15.1 years ago by ▴ 120
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1
reply
1.0k
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DESeq2 for ChIP on chip microarrays
deseq2 microarray nimblegene ratio limma
updated 8.1 years ago by 43k • written 8.1 years ago by ★ 1.5k
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4
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2.0k
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
limma deg microarray
updated 8.1 years ago by 53k • written 8.1 years ago by • 0
2
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4
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1.7k
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design microarrays limma
limma statistical power design variability microarray
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
4
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5
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3.0k
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Retrieving probes mapping to gene ID in microarray analysis
microarray affymetrix probeset probe
updated 8.1 years ago by ★ 6.6k • written 8.1 years ago by • 0
0
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5
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2.8k
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Is it possible to convert Methylumi object into RGChannelSet
microarray minfi methylumi illumina450k
9.0 years ago • updated 8.1 years ago poojitha.stemcell ▴ 10
28
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8
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14k
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Removing continuous covariate effects in limma analysis
limma microarray
updated 8.2 years ago by 53k • written 10.7 years ago by ▴ 160
1
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6
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1.7k
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two-color microarray - technical replicates
microarray limma TARGET FILE
8.3 years ago • updated 8.2 years ago Sanches • 0
0
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3
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2.0k
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How can I pre-process illumina raw file
illumina microarray
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 260
1
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1
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2.7k
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Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat microarray batch effects
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 10
0
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0
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1.7k
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Data format after removing batch effects using linear model vs using comBat
microarray SVA ComBat Linear models Residuals
8.3 years ago DataFanatic ▴ 10
7
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7
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2.5k
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Identify up and down regulated genes in affymetrix data
limma microarray affy
updated 8.3 years ago by ▴ 40 • written 8.3 years ago by • 0
0
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3
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2.2k
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Annotation to probes in mogene20sttranscriptcluster.db returns "NA"
mogene20sttranscriptcluster.db microarray
8.3 years ago haroon.maximas • 0
2
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2
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1.4k
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paCalls with Clariom Chips
oligo microarray clariom
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
2
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1
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1.3k
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Plotting Gene Expression Data From Multiple Batches
batch effect microarray plot
updated 8.4 years ago by ★ 2.0k • written 8.4 years ago by ▴ 100
3
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2
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1.5k
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RankProd throws "is.infinite(data)" error for type "S4" for differential expression analysis
rankprod limma affy bioconductor microarray
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 20
2
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1
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2.6k
views
How to get genes corresponding to a GO term from topGOData object?
topGO microarray R gene ontology
updated 8.4 years ago by ▴ 10 • written 9.7 years ago by ▴ 20
0
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0
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1.1k
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Jackknifing/bootstrapping input and output question
jackknifing R microarray bootstrap
8.4 years ago bhgyu ▴ 30
0
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1
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1.6k
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Annotation of Probe id to Gene
bioconductor annotate microarray arabidopsis thaliana
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
0
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2
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1.7k
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How to know which Microarray Technique was used to processes the files
R microarray affymetrix microarrays
updated 8.4 years ago by ★ 1.1k • written 8.4 years ago by • 0
6
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4
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3.5k
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Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
8.4 years ago rkp • 0
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1.2k
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Analyzing "Hitachi human oligo chip-drug responsive genes" platform data
microarray analysis
8.5 years ago arisarkar88 ▴ 40
0
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1
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1.1k
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How to extract DEG using limma at threshold value p<0.05 and fold change >1.5 ?
limma microarray R bioconductor
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
0
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1
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1.2k
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can't install GEOquery
microarray
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
3
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1
reply
1.8k
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Limma Model Design
limma methylation microarray
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
1
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6
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2.5k
views
Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 8.5 years ago by ★ 13k • written 8.5 years ago by • 0
2
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2
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1.8k
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around 2000 Affy probe set IDs cannot be mapped with Ensembl IDs by BiomaRt
microarray annotation biomart hgu133a
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
2
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5
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4.7k
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Limma toptable interpretation check
limma microarray fdr p-value results
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 30
0
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0
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737
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queries reg hub genes
normalization limma microarray annotation
8.5 years ago krithi11987 • 0
1
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1
reply
2.5k
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 8.5 years ago by ▴ 420 • written 8.5 years ago by ▴ 30
4
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7
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5.4k
views
Alternative packages to limma for analysis of microarray datasets
limma microarray deg
updated 8.5 years ago by ▴ 610 • written 8.5 years ago by ▴ 10
0
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7
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2.7k
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Help with diff. expression analysis of Agilent files
microarray agilent differential gene expression R
updated 8.5 years ago by ★ 1.1k • written 8.5 years ago by ▴ 30
2,319 results • Page 6 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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