Showing : affymetrix • reset
5
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9
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4.2k
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Looking for annotation file for Affymetrix SNP 6.0
copynumber snp affymetrix
8.5 years ago • updated 8.4 years ago KB ▴ 50
2
votes
6
replies
1.6k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast limma pathway analysis differential gene expression affymetrix
9.1 years ago svlachavas ▴ 830
3
votes
15
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2.7k
views
Are the p-values supposed to be on the order of 10^-120?
limma affy bioconductor affymetrix
updated 9.6 years ago by 50k • written 9.6 years ago by • 0
6
votes
5
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1.8k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes expression affymetrix pd.hugene.2.0.st limma
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 200
2
votes
4
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2.2k
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Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix limma filtering
updated 9.0 years ago by 65k • written 9.0 years ago by • 0
0
votes
1
reply
1.4k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 4.5 years ago by • 0 • written 5.3 years ago by ★ 3.9k
0
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1
reply
2.0k
views
RNA degradation plot: why curves are so smooth?
normalization microarray affymetrix
updated 9.3 years ago by 65k • written 9.3 years ago by • 0
2
votes
2
replies
1.0k
views
Is it possible some statistical evaluation with a few replicates and one control in microarray data analysis in r
r bioconductor affymetrix differential gene expression
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 830
0
votes
2
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1.6k
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Possible Data integration of molecular data(transcriptomic) and imaging data from the same patients in R
data integration microarray bioconductor affymetrix biomarkers
updated 9.2 years ago by ★ 13k • written 9.2 years ago by ▴ 830
5
votes
5
replies
1.2k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools huex10sttranscriptcluster.db affymetrix Geoquery
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 830
3
votes
4
replies
1.5k
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AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
1
reply
2.0k
views
How to plot the RMA log2 normalised data from Affymetrix
log2 RMA Affymetrix affy Normalization
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
0
votes
1
reply
879
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
2
replies
1.8k
views
How to convert .CEL file to .VCF file?
vcf cell affymetrix
2.9 years ago jesus • 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
1
vote
2
replies
825
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Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
23 months ago Mikołaj Mierzejewski • 0
3
votes
1
reply
1.6k
views
what is fitProbeLevelModel()? doing
affymetrix oligo microarray
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 20
0
votes
1
reply
1.8k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray affymetrix oligo RMA normalization
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 20
3
votes
8
replies
2.3k
views
Error aroma.affymetrix [affxparser Fusion SDK exception]
affymetrix affxparser
updated 8.4 years ago by ★ 2.4k • written 8.4 years ago by ▴ 40
0
votes
3
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1.5k
views
frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
frma affymetrix barcode
updated 8.3 years ago by ▴ 830 • written 8.3 years ago by • 0
1
vote
5
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1.8k
views
Filtering genes with missing Entrez ID using "nsFilter"
nsfilter affymetrix hugene10sttranscriptcluster.db annotation
updated 7.2 years ago by 65k • written 7.2 years ago by • 0
6
votes
7
replies
3.2k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo affycoretools hta2.0 affymetrix
updated 24 months ago by ▴ 10 • written 7.1 years ago by ▴ 830
0
votes
2
replies
1.4k
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Quality control for Affymetrix GeneChip Mouse Gene 2.0 ST Array
qc qualitycontrol arrayqualitymetrics mouse gene st 2.0 affymetrix
updated 6.7 years ago by 65k • written 6.7 years ago by • 0
4
votes
5
replies
2.3k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray affymetrix probeset probe
updated 6.6 years ago by ★ 6.5k • written 6.6 years ago by • 0
0
votes
1
reply
917
views
Affy Mouse Annotation
annotation affymetrix
updated 6.1 years ago by 65k • written 6.1 years ago by • 0
3
votes
3
replies
1.1k
views
Limma: Don't have .CEL Affymatrix Files.
limma affymetrix
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 10
0
votes
1
reply
719
views
differential expression analysis of rice
microarray differential expression analysis GPL2025 affymetrix
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
0
votes
7
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2.0k
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Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix Illumina probes microarray annotation package
updated 5.0 years ago by ★ 3.9k • written 5.0 years ago by • 0
0
votes
3
replies
700
views
Input files for Affymetrix platform
Affymetrix CEL TXT
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 50
0
votes
0
replies
983
views
Remove coexpressed gene pair modules using eisa package
isa2 eisa microarray affymetrix
9.0 years ago dhwani.dholakia • 0
0
votes
1
reply
1.2k
views
Filtering out lowly expressed genes on Affymetrix Gene ST arrays
Affymetrix Gene ST limma
9.0 years ago knaxerova ▴ 10
0
votes
0
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1.4k
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News: Rebuilding annotation packages for Affymetrix Gene/Exon ST Arrays
affymetrix annotation microarray News
8.9 years ago James W. MacDonald 65k
0
votes
1
reply
1.3k
views
extract raw expression values in oligo package
oligo affymetrix raw expression
8.7 years ago queso012 • 0
0
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0
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2.2k
views
MAplot: Binning grid too coarse for current (small) bandwidth
affy affymetrix affymetrics affymetrixchip
9.3 years ago neverstop • 0
0
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0
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1.1k
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QC for Affymetrix Arrays
affymetrix affymetrix microarrays aroma
7.9 years ago gaiusjaugustus • 0
0
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1
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1.2k
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Finding/Understanding Affy 6.0 Annotation File
affy affymetrix microarray SNP
5.7 years ago CantExitVIM ▴ 10
36 results • Page 1 of 1
Recent ...
Replies
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by nbay13 • 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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