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Affymetrix
•
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1
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2
replies
667
views
Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
18 months ago
Mikołaj Mierzejewski
• 0
1
vote
2
replies
857
views
Affymetrix analysis of microarray by using Limma
limma
MicroarrayData
Microarray
Affymetrix
18 months ago
Mikołaj Mierzejewski
• 0
0
votes
2
replies
1.5k
views
How to convert .CEL file to .VCF file?
vcf
cell
affymetrix
2.5 years ago
jesus
• 0
0
votes
1
reply
732
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 2.6 years ago by
Guido Hooiveld
★ 3.8k • written 2.6 years ago by
Pierre-Alex
• 0
0
votes
1
reply
1.6k
views
How to plot the RMA log2 normalised data from Affymetrix
log2
RMA
Affymetrix
affy
Normalization
updated 2.8 years ago by
Kevin Blighe
3.9k • written 2.8 years ago by
Lara
• 0
3
votes
4
replies
1.2k
views
AnnotationData package for Affymetrix HT MG-430 PM Array Plate
RNAseq
Affymetrix
Mouse
updated 3.1 years ago by
Guido Hooiveld
★ 3.8k • written 3.1 years ago by
olrema
• 0
5
votes
5
replies
1.0k
views
Annotation issue while analyzing processed Affymetrix Human Exon 1.0 ST Arrays from Geoquery
affycoretools
huex10sttranscriptcluster.db
affymetrix
Geoquery
updated 3.7 years ago by
James W. MacDonald
64k • written 3.7 years ago by
svlachavas
▴ 820
0
votes
3
replies
573
views
Input files for Affymetrix platform
Affymetrix
CEL
TXT
updated 4.0 years ago by
James W. MacDonald
64k • written 4.0 years ago by
pbachali
▴ 50
0
votes
1
reply
1.2k
views
Is GCRMA normalization possible with oligo?
oligo
pd.moe430a
gcrma
affymetrix
normalization
updated 4.0 years ago by
Rise
• 0 • written 4.9 years ago by
Guido Hooiveld
★ 3.8k
0
votes
7
replies
1.7k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix
Illumina
probes
microarray
annotation package
updated 4.6 years ago by
Guido Hooiveld
★ 3.8k • written 4.6 years ago by
naf
• 0
0
votes
1
reply
621
views
differential expression analysis of rice
microarray
differential expression analysis
GPL2025
affymetrix
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
pratikshasharma47
• 0
3
votes
3
replies
994
views
Limma: Don't have .CEL Affymatrix Files.
limma
affymetrix
updated 5.2 years ago by
Gordon Smyth
48k • written 5.2 years ago by
CantExitVIM
▴ 10
0
votes
1
reply
1.0k
views
Finding/Understanding Affy 6.0 Annotation File
affy
affymetrix
microarray
SNP
5.3 years ago
CantExitVIM
▴ 10
0
votes
1
reply
789
views
Affy Mouse Annotation
annotation
affymetrix
updated 5.7 years ago by
James W. MacDonald
64k • written 5.7 years ago by
trhood
• 0
4
votes
5
replies
2.0k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray
affymetrix
probeset
probe
updated 6.2 years ago by
Mike Smith
★ 6.2k • written 6.2 years ago by
n.lu
• 0
0
votes
2
replies
1.3k
views
Quality control for Affymetrix GeneChip Mouse Gene 2.0 ST Array
qc
qualitycontrol
arrayqualitymetrics
mouse gene st 2.0
affymetrix
updated 6.3 years ago by
James W. MacDonald
64k • written 6.3 years ago by
n.lu
• 0
6
votes
7
replies
3.0k
views
Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with oligo for DE analysis
oligo
affycoretools
hta2.0
affymetrix
updated 18 months ago by
Yang Shi
▴ 10 • written 6.7 years ago by
svlachavas
▴ 820
1
vote
5
replies
1.6k
views
Filtering genes with missing Entrez ID using "nsFilter"
nsfilter
affymetrix
hugene10sttranscriptcluster.db annotation
updated 6.8 years ago by
James W. MacDonald
64k • written 6.8 years ago by
hallie.cla
• 0
0
votes
0
replies
964
views
QC for Affymetrix Arrays
affymetrix
affymetrix microarrays
aroma
7.5 years ago
gaiusjaugustus
• 0
0
votes
3
replies
1.4k
views
frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
frma
affymetrix
barcode
updated 7.9 years ago by
Matthew McCall
▴ 830 • written 7.9 years ago by
minnie
• 0
3
votes
8
replies
2.1k
views
Error aroma.affymetrix [affxparser Fusion SDK exception]
affymetrix
affxparser
updated 8.0 years ago by
Henrik Bengtsson
★ 2.4k • written 8.0 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
1
reply
1.7k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray
affymetrix
oligo
RMA
normalization
updated 8.0 years ago by
James W. MacDonald
64k • written 8.0 years ago by
Nathaniel
▴ 20
3
votes
1
reply
1.4k
views
what is fitProbeLevelModel()? doing
affymetrix
oligo
microarray
updated 8.0 years ago by
James W. MacDonald
64k • written 8.0 years ago by
Nathaniel
▴ 20
5
votes
9
replies
3.9k
views
Looking for annotation file for Affymetrix SNP 6.0
copynumber
snp
affymetrix
8.0 years ago
KB
▴ 50
0
votes
1
reply
1.2k
views
extract raw expression values in oligo package
oligo
affymetrix
raw expression
8.3 years ago
queso012
• 0
0
votes
0
replies
1.3k
views
News:
Rebuilding annotation packages for Affymetrix Gene/Exon ST Arrays
affymetrix
annotation
microarray
News
8.5 years ago
James W. MacDonald
64k
0
votes
1
reply
1.1k
views
Filtering out lowly expressed genes on Affymetrix Gene ST arrays
Affymetrix
Gene ST
limma
8.5 years ago
knaxerova
▴ 10
0
votes
0
replies
918
views
Remove coexpressed gene pair modules using eisa package
isa2
eisa
microarray
affymetrix
8.6 years ago
dhwani.dholakia
• 0
2
votes
4
replies
2.0k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix
limma
filtering
updated 8.6 years ago by
James W. MacDonald
64k • written 8.6 years ago by
ablanchetcohen
• 0
2
votes
6
replies
1.5k
views
Appropriate use of the function mroast to find KEGG pathways for differential expression
mroast
limma
pathway analysis
differential gene expression
affymetrix
8.7 years ago
svlachavas
▴ 820
0
votes
2
replies
1.5k
views
Possible Data integration of molecular data(transcriptomic) and imaging data from the same patients in R
data integration
microarray
bioconductor
affymetrix
biomarkers
updated 8.7 years ago by
Wolfgang Huber
13k • written 8.7 years ago by
svlachavas
▴ 820
2
votes
2
replies
954
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 8.8 years ago by
James W. MacDonald
64k • written 8.8 years ago by
svlachavas
▴ 820
0
votes
0
replies
2.1k
views
MAplot: Binning grid too coarse for current (small) bandwidth
affy
affymetrix
affymetrics
affymetrixchip
8.9 years ago
neverstop
• 0
6
votes
5
replies
1.6k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes
expression
affymetrix
pd.hugene.2.0.st
limma
updated 8.9 years ago by
Gordon Smyth
48k • written 8.9 years ago by
Paulo Nuin
▴ 200
0
votes
1
reply
1.9k
views
RNA degradation plot: why curves are so smooth?
normalization
microarray
affymetrix
updated 8.9 years ago by
James W. MacDonald
64k • written 8.9 years ago by
neverstop
• 0
3
votes
15
replies
2.5k
views
Are the p-values supposed to be on the order of 10^-120?
limma
affy
bioconductor
affymetrix
updated 9.1 years ago by
Gordon Smyth
48k • written 9.1 years ago by
mccallionc403
• 0
36 results • Page
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Comment: Ensembl down???
by
James W. MacDonald
64k
I normally caution against mapping between annotation sources (NCBI and Ensembl), as it usually doesn't work well. However, it is possible.…
Answer: NCBI protein conversion to CDNA and NCBI gene (in R)
by
James W. MacDonald
64k
I already showed you how to do this for gene symbols, and it's analogous for any other annotation ID. Please see the `AnnotationDbi` [vigne…
Comment: Obtaining rsIDs with ENSG and variant ID information
by
Robert Castelo
★ 3.0k
This is a large package, and when downloading and installing large packages it's often the case to get timeouts. Try setting a longer time …
Comment: How does Deseq2 deal with the row with zero when calculating size factors
by
ATpoint
★ 3.6k
> Because I found that if there is at least one gene without zero among all of the samples, the deseq2 runs smoothly. No, it doesn't. ``…
Comment: Obtaining rsIDs with ENSG and variant ID information
by
bd2000
• 0
Thank you for your answer. I've tried to download the package but it didn't work: Error in download.file(url, destfile, method, mode =…
Votes
Answer: biomaRt not working - lazy table error
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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