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affymetrix
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1
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820
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Problem with results of Differential expression in Affymetrix microarray
limma
MicroarrayData
Microarray
Affymetrix
23 months ago
Mikołaj Mierzejewski
• 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
0
votes
2
replies
1.8k
views
How to convert .CEL file to .VCF file?
vcf
cell
affymetrix
2.9 years ago
jesus
• 0
0
votes
1
reply
873
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3.1 years ago by
Guido Hooiveld
★ 3.9k • written 3.1 years ago by
Pierre-Alex
• 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
Kevin Blighe
★ 3.9k • written 3.2 years ago by
Lara
• 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
Guido Hooiveld
★ 3.9k • written 3.5 years ago by
olrema
• 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
James W. MacDonald
65k • written 4.1 years ago by
svlachavas
▴ 830
0
votes
3
replies
697
views
Input files for Affymetrix platform
Affymetrix
CEL
TXT
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
pbachali
▴ 50
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
Rise
• 0 • written 5.3 years ago by
Guido Hooiveld
★ 3.9k
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
Guido Hooiveld
★ 3.9k • written 5.0 years ago by
naf
• 0
0
votes
1
reply
716
views
differential expression analysis of rice
microarray
differential expression analysis
GPL2025
affymetrix
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
pratikshasharma47
• 0
3
votes
3
replies
1.1k
views
Limma: Don't have .CEL Affymatrix Files.
limma
affymetrix
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
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
910
views
Affy Mouse Annotation
annotation
affymetrix
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
trhood
• 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
Mike Smith
★ 6.5k • written 6.6 years ago by
n.lu
• 0
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
James W. MacDonald
65k • written 6.7 years ago by
n.lu
• 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 23 months ago by
Yang Shi
▴ 10 • written 7.1 years ago by
svlachavas
▴ 830
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
James W. MacDonald
65k • written 7.2 years ago by
hallie.cla
• 0
0
votes
0
replies
1.1k
views
QC for Affymetrix Arrays
affymetrix
affymetrix microarrays
aroma
7.9 years ago
gaiusjaugustus
• 0
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
Matthew McCall
▴ 830 • written 8.3 years ago by
minnie
• 0
3
votes
8
replies
2.3k
views
Error aroma.affymetrix [affxparser Fusion SDK exception]
affymetrix
affxparser
updated 8.4 years ago by
Henrik Bengtsson
★ 2.4k • written 8.4 years ago by
Vinicius Henrique da Silva
▴ 40
0
votes
1
reply
1.8k
views
PLIER normalization for Affymetrix GeneChip arrays?
microarray
affymetrix
oligo
RMA
normalization
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
Nathaniel
▴ 20
3
votes
1
reply
1.6k
views
what is fitProbeLevelModel()? doing
affymetrix
oligo
microarray
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
Nathaniel
▴ 20
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
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
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
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
replies
981
views
Remove coexpressed gene pair modules using eisa package
isa2
eisa
microarray
affymetrix
9.0 years ago
dhwani.dholakia
• 0
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
James W. MacDonald
65k • written 9.0 years ago by
ablanchetcohen
• 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
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
Wolfgang Huber
★ 13k • written 9.1 years ago by
svlachavas
▴ 830
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
James W. MacDonald
65k • written 9.2 years ago by
svlachavas
▴ 830
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
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
Gordon Smyth
50k • written 9.3 years ago by
Paulo Nuin
▴ 200
0
votes
1
reply
2.0k
views
RNA degradation plot: why curves are so smooth?
normalization
microarray
affymetrix
updated 9.3 years ago by
James W. MacDonald
65k • written 9.3 years ago by
neverstop
• 0
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
Gordon Smyth
50k • written 9.6 years ago by
mccallionc403
• 0
36 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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