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affymetrixchip
•
reset
5
votes
9
replies
3.1k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor
expresiondataset
affymetrixchip
differential gene expression
9.1 years ago
svlachavas
▴ 830
4
votes
10
replies
1.9k
views
Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
pd.hg.u219
Microarray
oligo
AffymetrixChip
23 months ago
Yang Shi
▴ 10
3
votes
11
replies
3.5k
views
Filtering on present/absent calls methodology and perfect match only arrays
bioconductor
mas5
perfectmatch
affymetrixchip
filter
updated 9.2 years ago by
James W. MacDonald
65k • written 9.2 years ago by
svlachavas
▴ 830
3
votes
2
replies
1.5k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi
mouse4302
affymetrixchip
annotationdata
R
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
koreebay
• 0
2
votes
2
replies
849
views
How to compute P/A calls at gene-level probeset of Human Gene 1.0 ST Array
pd.hugene.1.0.st.v1
oligo
AffymetrixChip
22 months ago
Yang Shi
▴ 10
2
votes
2
replies
640
views
Question about transforming log expression values to antilog values in limma
IlluminaChip
limma
AffymetrixChip
Normalization
Microarray
12 months ago
Abdul
▴ 20
2
votes
2
replies
969
views
Subscript out of bounds while normalising using affy::rma()
Normalization
affy
AffymetrixChip
2.9 years ago
geoffrey
▴ 10
2
votes
4
replies
1.1k
views
Robust Multi-array Average could get negative value or not?
pd.hg.u219
oligo
AffymetrixChip
23 months ago
Yang Shi
▴ 10
2
votes
5
replies
1.0k
views
Equivalence between PSDABG and Logarithmic Intensity Error (PLIER) Estimation
pd.hugene.1.0.st.v1
oligo
AffymetrixChip
22 months ago
Yang Shi
▴ 10
2
votes
2
replies
544
views
2-Way Repeated Measures ANOVA - Affymetrix
AffymetrixChip
MicroarrayData
Anova
18 months ago
evan.j.williams
▴ 10
2
votes
5
replies
2.9k
views
miRNA expression analysis : annotation
miRNA
annotation
affymetrixchip
9.0 years ago
aswathym
▴ 10
1
vote
4
replies
3.4k
views
GeneChip Human Transcriptome Array 2.0 analysis in R for identifying possible differential exon splicing events
affymetrixchip
GenechipHumanTranscriptomeArray2.0
exon array analysis
9.1 years ago
svlachavas
▴ 830
1
vote
3
replies
1.5k
views
BioNet package network analysis important questions for tutorial
BioNet
bioconductor
affymetrixchip
network analysis
9.1 years ago
svlachavas
▴ 830
1
vote
1
reply
743
views
Strange error with RMA during Affymetrix data analysis
AffymetrixChip
RMA
updated 17 months ago by
Mike Smith
★ 6.5k • written 17 months ago by
Sara
▴ 10
1
vote
4
replies
643
views
How to annotate mir4.1 arrays?
AffymetrixChip
miRNA
oligo
11 months ago • updated 8 months ago
richardallenfriedmanbrooklyn
▴ 20
1
vote
2
replies
472
views
Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db
hgu133plus2hsentrezg.db
chiptype
chipster
hgu133plus2.db
AffymetrixChip
10 months ago
alexia.brunel
• 0
0
votes
4
replies
360
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
4 weeks ago • updated 24 days ago
Efra
• 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
1.2k
views
Correst use of GeneOverlap R Package
GeneOverlap
DEGgenes
affymetrixchip
bioconductor
9.0 years ago
svlachavas
▴ 830
0
votes
4
replies
2.3k
views
HUgene 2.0 analyses heatmap
hugene20
heatmap
affymetrixchip
updated 8.9 years ago by
alakatos
▴ 130 • written 8.9 years ago by
kanacska
▴ 10
0
votes
2
replies
735
views
How to extract probe level intensity after rma() normalization
MicroarrayData
AffymetrixChip
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
Haoran
• 0
0
votes
1
reply
858
views
Microarray: Build annotation for HT MG430PM affymetrix
AffymetrixChip
Microarray
affymetrix
updated 3.0 years ago by
Guido Hooiveld
★ 3.9k • written 3.0 years ago by
Pierre-Alex
• 0
0
votes
1
reply
463
views
Affymetrix hgu133plus2.db: How to best derive an expression value for genes that map to multiple probe ids
affydata
hgu133plus2.db
AffymetrixChip
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
Matthias Munz
▴ 10
0
votes
4
replies
894
views
getProbeInfo and exprs return two different dimensions
CELfile
MicroarrayData
AffymetrixChip
2.1 years ago
Haoran
• 0
0
votes
0
replies
498
views
Volcano plot
limma
AffymetrixChip
11 months ago
e.gunaut
• 0
0
votes
1
reply
1.9k
views
Having trouble with new brainarray CDF
Microarray
Annotation
AnnotationData
AffymetrixChip
hgu133a2
cdf
probe
graph
AnnotationDbi
updated 13.0 years ago by
Marc Carlson
★ 7.2k • written 13.0 years ago by
Martha Behnke
▴ 100
26 results • Page
1 of 1
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Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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