Showing : probe • reset
0
votes
11
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2.6k
views
globaltest question
Pathways probe affy Pathways probe affy
written 18.5 years ago by ▴ 30
2
votes
2
replies
7.0k
views
log transform in RMA normalization
Normalization probe Normalization probe
updated 2.5 years ago by ▴ 200 • written 12.1 years ago by ▴ 440
0
votes
0
replies
696
views
Filtering single-channel Affymetrix probes
filtering probe MicroarrayData
2.5 years ago Fatemeh • 0
0
votes
1
reply
1.6k
views
filtering on variance
probe affy probe affy
updated 3.9 years ago by 52k • written 17.2 years ago by ▴ 90
0
votes
0
replies
916
views
Probe Design questions
probe affy
4.4 years ago henry1995910343 • 0
4
votes
10
replies
3.5k
views
how to analyze WGCNA results?
cancer probe deseq2 annotation normalization
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
0
votes
8
replies
5.5k
views
Combining 2 datasets from 2 different RNAseq experiments
deseq2 normalization probe
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
0
replies
588
views
Program to calculate genetic distances with long sequences
probe go
5.0 years ago antoniorevail • 0
0
votes
5
replies
1.4k
views
Does anyone have experience using the massiR package?
massiR microarray R probe
5.5 years ago Steve Lowe ▴ 30
0
votes
0
replies
736
views
massiR Extracting and Plotting Y Chr Probe Data
probe microarray
5.5 years ago Steve Lowe ▴ 30
0
votes
1
reply
911
views
Determining survival correlation among probes
annotation probe microarray
5.6 years ago sbrackett007 • 0
0
votes
4
replies
1.5k
views
Cannot down load the "org.Hs.eg.db" completely
software error probe
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
2
votes
4
replies
1.5k
views
SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC probe normalization GEOdata cancer
5.9 years ago s.goncalvesclaro ▴ 10
0
votes
2
replies
2.5k
views
liftover probe annotation from hg19 to hg38 for methylation array data using minfi (EPIC methylation array data)
annotation probe software error EPIC methylation array
5.9 years ago brendan.miller • 0
1
vote
3
replies
946
views
I can't install the package "matchprobes"
software error probe
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
0
replies
863
views
How to merging multiple GSEs with different GPLs?
microarray probe R
6.1 years ago maryam.sabet • 0
0
votes
1
reply
1.4k
views
MCLUST: finding the best number of Gaussian components to fit my data
software error microarray probe annotation
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
0
votes
0
replies
1.3k
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe affy probe affy
updated 6.1 years ago by 0 • written 21.1 years ago by ▴ 940
0
votes
3
replies
4.7k
views
Use probesets with highest baseline expression for differential gene
Annotation probe limma
13.0 years ago • updated 6.5 years ago Gordon Smyth 52k
1
vote
2
replies
1.2k
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays microarray probe statistics
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
2
replies
2.1k
views
[ComBat] ComBat outputting NAs with Large Batches - Switch to Log Likelihood
probe probe
updated 6.9 years ago by • 0 • written 12.3 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Probe annotations for ABI Human Genome Survey V2 microarray using Oracle
annotation probe microarray abi human genome survey v2 Oracle
7.0 years ago judemtaylor • 0
1
vote
3
replies
2.4k
views
GO terms: Annotation for HumanMethylation450
Annotation GO probe Annotation GO probe
updated 7.0 years ago by • 0 • written 11.9 years ago by ▴ 970
0
votes
1
reply
1.3k
views
index of probes in Illumina Infinium MethylationEPIC BeadChip
probe
7.1 years ago mcarmel • 0
4
votes
5
replies
2.7k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray affymetrix probeset probe
updated 7.4 years ago by ★ 6.6k • written 7.4 years ago by • 0
0
votes
1
reply
1.5k
views
Multiple samples on the same graph
Pathview probe
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by • 0
0
votes
1
reply
1.1k
views
probe set-gene relation
probe geneid probeset
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
0
votes
8
replies
2.3k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 7.9 years ago by ▴ 40 • written 18.5 years ago by ▴ 20
1
vote
6
replies
2.0k
views
Remove a list of specific probes from an HTAFeatureSet
pd.clariom.d.human affy probe
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 40
1
vote
5
replies
1.3k
views
Filter out ranges by number of probes
probe ranges
updated 8.0 years ago by ★ 6.6k • written 8.0 years ago by ▴ 30
0
votes
0
replies
1.3k
views
removing probes representing in a certain beads
minfi probe preprocessing
8.1 years ago niutster • 0
0
votes
4
replies
2.1k
views
minfi probe removal
minfi probe
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
3
votes
4
replies
5.4k
views
LIMMA and Agilent single color
Annotation probe limma agilent
14.2 years ago • updated 8.1 years ago Gordon Smyth 52k
0
votes
1
reply
2.0k
views
LIMMA and Agilent single color
probe limma probe limma
updated 8.1 years ago by 52k • written 14.2 years ago by ▴ 60
1
vote
4
replies
2.4k
views
How to install old GenomicRanges 1.14.4 package ?
bioconductor R cancer probe deseq2
updated 8.8 years ago by ▴ 10 • written 8.8 years ago by • 0
0
votes
1
reply
1.5k
views
'could not find function "R (>= 2.1"' while trying https://bioconductor.org/packages/3.2/bioc, trying https://bioconductor.org/packages/3.1/bioc …
cancer probe microarray
updated 8.9 years ago by 25k • written 8.9 years ago by • 0
0
votes
1
reply
1.6k
views
Importing and Extracting Annotation
annotation zebrafish probe
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
2
votes
3
replies
2.1k
views
i need AGI code as my probset
affy cdf probe
9.3 years ago • updated 9.1 years ago Angel ▴ 40
0
votes
5
replies
1.9k
views
"oligo" package: probenames/probeinfo different from expr-set (read.cellfles): miRNA 4.0 (affy)
microarray probe annotation affy
9.1 years ago dietmar.pils • 0
0
votes
0
replies
1.3k
views
Help for affy
affy process probe
9.1 years ago weizhong_2007 • 0
0
votes
3
replies
12k
views
How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 9.6 years ago by ▴ 840 • written 9.6 years ago by ▴ 10
1
vote
4
replies
1.7k
views
mutually add a tab in the beggining of the header to make it a valid RMA format
software error probe affy RMA
9.6 years ago Angel ▴ 40
2
votes
2
replies
3.0k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe annotation illimina 450k methylation minfi methylation
9.7 years ago metamaden ▴ 10
0
votes
5
replies
5.8k
views
How to do Affy ST array analysis
Annotation Normalization hgu133a probe affy oligo Annotation Normalization hgu133a probe
updated 9.8 years ago by • 0 • written 10.8 years ago by ★ 13k
0
votes
1
reply
1.7k
views
simpleaffy segmentation fault
Survival probe genefilter affy affyio Survival probe genefilter affy affyio
updated 9.8 years ago by • 0 • written 18.2 years ago by ▴ 170
0
votes
2
replies
1.3k
views
difficulty in mapping gene names to probes coordinates in a celfile
microarray probe
updated 10.0 years ago by 68k • written 10.0 years ago by • 0
0
votes
2
replies
1.9k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 10.0 years ago by • 0 • written 20.4 years ago by ▴ 600
0
votes
3
replies
3.0k
views
filtering out probes with no gene symbol from expressionSet
probe filter subset gene symbol affy
10.0 years ago alakatos ▴ 130
1
vote
1
reply
2.0k
views
Coercion of MethyLumiSet to MethyLumiR changes raw methylation values?
Normalization probe lumi Normalization probe lumi
updated 10.1 years ago by • 0 • written 11.0 years ago by ▴ 20
1
vote
2
replies
2.0k
views
array quality control, affy probes, contracts setting in limma, result interpretation and weights
limma affy probe qualitycontrol design and contrast matrix
updated 10.2 years ago by 52k • written 10.2 years ago by ▴ 130
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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