Showing : affymetrix • reset
3
votes
15
replies
2.7k
views
Are the p-values supposed to be on the order of 10^-120?
limma affy bioconductor affymetrix
updated 9.5 years ago by 50k • written 9.5 years ago by • 0
5
votes
9
replies
4.2k
views
Looking for annotation file for Affymetrix SNP 6.0
copynumber snp affymetrix
8.4 years ago KB ▴ 50
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
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 23 months ago by ▴ 10 • written 7.1 years ago by ▴ 830
0
votes
7
replies
2.0k
views
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
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
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
6
votes
5
replies
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
1
vote
5
replies
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
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
2
votes
4
replies
2.2k
views
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
3
votes
4
replies
1.4k
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq Affymetrix Mouse
updated 3.5 years ago by ★ 3.9k • written 3.5 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
3
replies
685
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
3
replies
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
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
replies
1.6k
views
Possible Data integration of molecular data(transcriptomic) and imaging data from the same patients in R
data integration microarray bioconductor affymetrix biomarkers
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 830
0
votes
2
replies
1.4k
views
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
0
votes
2
replies
1.7k
views
How to convert .CEL file to .VCF file?
vcf cell affymetrix
2.9 years ago • updated 2.8 years ago jesus • 0
1
vote
2
replies
1.1k
views
Affymetrix analysis of microarray by using Limma
limma MicroarrayData Microarray Affymetrix
22 months ago Mikołaj Mierzejewski • 0
1
vote
2
replies
808
views
Problem with results of Differential expression in Affymetrix microarray
limma MicroarrayData Microarray Affymetrix
22 months ago Mikołaj Mierzejewski • 0
0
votes
1
reply
1.3k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 4.4 years ago by • 0 • written 5.3 years ago by ★ 3.9k
0
votes
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
0
votes
1
reply
1.2k
views
Filtering out lowly expressed genes on Affymetrix Gene ST arrays
Affymetrix Gene ST limma
8.9 years ago knaxerova ▴ 10
0
votes
1
reply
1.3k
views
extract raw expression values in oligo package
oligo affymetrix raw expression
8.7 years ago queso012 • 0
3
votes
1
reply
1.5k
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
0
votes
1
reply
905
views
Affy Mouse Annotation
annotation affymetrix
updated 6.1 years ago by 65k • written 6.1 years ago by • 0
0
votes
1
reply
1.2k
views
Finding/Understanding Affy 6.0 Annotation File
affy affymetrix microarray SNP
5.7 years ago CantExitVIM ▴ 10
0
votes
1
reply
711
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
1
reply
1.9k
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
862
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip Microarray affymetrix
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
0
votes
0
replies
2.2k
views
MAplot: Binning grid too coarse for current (small) bandwidth
affy affymetrix affymetrics affymetrixchip
9.3 years ago neverstop • 0
0
votes
0
replies
1.4k
views
News: Rebuilding annotation packages for Affymetrix Gene/Exon ST Arrays
affymetrix annotation microarray News
8.9 years ago James W. MacDonald 65k
0
votes
0
replies
1.1k
views
QC for Affymetrix Arrays
affymetrix affymetrix microarrays aroma
7.9 years ago gaiusjaugustus • 0
0
votes
0
replies
976
views
Remove coexpressed gene pair modules using eisa package
isa2 eisa microarray affymetrix
9.0 years ago dhwani.dholakia • 0
36 results • Page 1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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