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Affymetrix
•
reset
1
vote
2
replies
1.0k
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
2.5 years ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
1.4k
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
2.5 years ago
Mikołaj Mierzejewski
• 0
0
votes
2
replies
2.2k
views
How to convert .CEL file to .VCF file?
vcf
cell
affymetrix
3.5 years ago
jesus
• 0
0
votes
1
reply
1.1k
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3.7 years ago by
Guido Hooiveld
★ 4.1k • written 3.7 years ago by
Pierre-Alex
• 0
0
votes
1
reply
2.6k
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 3.8 years ago by
Kevin Blighe
★ 4.0k • written 3.8 years ago by
Lara
• 0
3
votes
4
replies
1.8k
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq
Affymetrix
Mouse
updated 4.2 years ago by
Guido Hooiveld
★ 4.1k • written 4.2 years ago by
olrema
• 0
5
votes
5
replies
1.5k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools
huex10sttranscriptcluster.db
affymetrix
Geoquery
updated 4.7 years ago by
James W. MacDonald
67k • written 4.7 years ago by
svlachavas
▴ 840
0
votes
3
replies
918
views
Input files for Affymetrix platform
Affymetrix
CEL
TXT
updated 5.0 years ago by
James W. MacDonald
67k • written 5.0 years ago by
pbachali
▴ 50
0
votes
1
reply
1.6k
views
Is GCRMA normalization possible with oligo?
oligo
pd.moe430a
gcrma
affymetrix
normalization
updated 5.1 years ago by
Rise
• 0 • written 5.9 years ago by
Guido Hooiveld
★ 4.1k
0
votes
7
replies
2.4k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix
Illumina
probes
microarray
annotation package
updated 5.6 years ago by
Guido Hooiveld
★ 4.1k • written 5.6 years ago by
naf
• 0
0
votes
1
reply
855
views
differential expression analysis of rice
microarray
differential expression analysis
GPL2025
affymetrix
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
pratikshasharma47
• 0
3
votes
3
replies
1.3k
views
Limma: Don't have .CEL Affymatrix Files.
limma
affymetrix
updated 6.2 years ago by
Gordon Smyth
52k • written 6.2 years ago by
CantExitVIM
▴ 10
0
votes
1
reply
1.5k
views
Finding/Understanding Affy 6.0 Annotation File
affy
affymetrix
microarray
SNP
6.4 years ago
CantExitVIM
▴ 10
0
votes
1
reply
1.1k
views
Affy Mouse Annotation
annotation
affymetrix
updated 6.7 years ago by
James W. MacDonald
67k • written 6.7 years ago by
trhood
• 0
4
votes
5
replies
2.6k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray
affymetrix
probeset
probe
updated 7.2 years ago by
Mike Smith
★ 6.6k • written 7.2 years ago by
n.lu
• 0
0
votes
2
replies
1.7k
views
Quality control for Affymetrix GeneChip Mouse Gene 2.0 ST Array
qc
qualitycontrol
arrayqualitymetrics
mouse gene st 2.0
affymetrix
updated 7.3 years ago by
James W. MacDonald
67k • written 7.3 years ago by
n.lu
• 0
6
votes
7
replies
3.6k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 2.6 years ago by
Yang Shi
▴ 10 • written 7.7 years ago by
svlachavas
▴ 840
1
vote
5
replies
2.1k
views
Filtering genes with missing Entrez ID using "nsFilter"
nsfilter
affymetrix
hugene10sttranscriptcluster.db annotation
updated 7.8 years ago by
James W. MacDonald
67k • written 7.8 years ago by
hallie.cla
• 0
0
votes
0
replies
1.2k
views
QC for Affymetrix Arrays
affymetrix
affymetrix microarrays
aroma
8.5 years ago
gaiusjaugustus
• 0
0
votes
3
replies
1.8k
views
frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
frma
affymetrix
barcode
updated 8.9 years ago by
Matthew McCall
▴ 830 • written 8.9 years ago by
minnie
• 0
3
votes
8
replies
2.7k
views
Error aroma.affymetrix [affxparser Fusion SDK exception]
affymetrix
affxparser
updated 9.0 years ago by
Henrik Bengtsson
★ 2.4k • written 9.0 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
1
reply
2.0k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray
affymetrix
oligo
RMA
normalization
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
Nathaniel
▴ 20
3
votes
1
reply
1.8k
views
what is fitProbeLevelModel()? doing
affymetrix
oligo
microarray
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
Nathaniel
▴ 20
5
votes
9
replies
4.5k
views
Looking for annotation file for Affymetrix SNP 6.0
copynumber
snp
affymetrix
9.1 years ago • updated 9.0 years ago
KB
▴ 50
0
votes
1
reply
1.4k
views
extract raw expression values in oligo package
oligo
affymetrix
raw expression
9.3 years ago
queso012
• 0
0
votes
0
replies
1.6k
views
News:
Rebuilding annotation packages for Affymetrix Gene/Exon ST Arrays
affymetrix
annotation
microarray
News
9.6 years ago
James W. MacDonald
67k
0
votes
1
reply
1.3k
views
Filtering out lowly expressed genes on Affymetrix Gene ST arrays
Affymetrix
Gene ST
limma
9.6 years ago
knaxerova
▴ 10
0
votes
0
replies
1.1k
views
Remove coexpressed gene pair modules using eisa package
isa2
eisa
microarray
affymetrix
9.6 years ago
dhwani.dholakia
• 0
2
votes
4
replies
2.4k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix
limma
filtering
updated 9.6 years ago by
James W. MacDonald
67k • written 9.6 years ago by
ablanchetcohen
• 0
2
votes
6
replies
1.9k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast
limma
pathway analysis
differential gene expression
affymetrix
9.7 years ago
svlachavas
▴ 840
0
votes
2
replies
1.7k
views
Possible Data integration of molecular data(transcriptomic) and imaging data from the same patients in R
data integration
microarray
bioconductor
affymetrix
biomarkers
updated 9.8 years ago by
Wolfgang Huber
★ 13k • written 9.8 years ago by
svlachavas
▴ 840
2
votes
2
replies
1.1k
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 9.8 years ago by
James W. MacDonald
67k • written 9.8 years ago by
svlachavas
▴ 840
0
votes
0
replies
2.4k
views
MAplot: Binning grid too coarse for current (small) bandwidth
affy
affymetrix
affymetrics
affymetrixchip
9.9 years ago
neverstop
• 0
6
votes
5
replies
2.1k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes
expression
affymetrix
pd.hugene.2.0.st
limma
updated 9.9 years ago by
Gordon Smyth
52k • written 9.9 years ago by
Paulo Nuin
▴ 200
0
votes
1
reply
2.2k
views
RNA degradation plot: why curves are so smooth?
normalization
microarray
affymetrix
updated 10.0 years ago by
James W. MacDonald
67k • written 10.0 years ago by
neverstop
• 0
3
votes
15
replies
3.0k
views
Are the p-values supposed to be on the order of 10^-120?
limma
affy
bioconductor
affymetrix
updated 10.2 years ago by
Gordon Smyth
52k • written 10.2 years ago by
mccallionc403
• 0
36 results • Page
1 of 1
Recent ...
Replies
Comment: nightmare to make custom txdb for genomes from ToxoDB
by
James W. MacDonald
67k
Thanks Hervé! Very helpful. However, I believe that `keepStandardChromosomes` gets called by `gDNAx`, and it appears not to work correctly.…
Answer: nightmare to make custom txdb for genomes from ToxoDB
by
Hervé Pagès
16k
Is this for genome assembly TGA4? https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006565.2/ If that's the case then: ``` library(t…
Answer: nightmare to make custom txdb for genomes from ToxoDB
by
James W. MacDonald
67k
Your post title is misleading. You have no problem whatsoever generating the `TxDb`, the problem is using it with `gDNAx`, which attempts t…
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
Just fit a model `~condition + experiment` where `condition` has three levels A, B and C. Ideally, use limma and include duplicate correlat…
Comment: Error in get_anno_data(ontology) : ontology not supported yet...
by
GODseeker
• 0
thank u so much ,god bless u,my dear friend.
Votes
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
Comment: Feature Counts - potential bug with outfile.jcounts
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