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Showing :
probe
•
reset
0
votes
2
replies
4.8k
views
log transform in RMA normalization
Normalization
probe
Normalization
probe
updated 5 months ago by
snijesh
▴ 20 • written 10.0 years ago by
Jack Luo
▴ 440
0
votes
0
replies
112
views
Filtering single-channel Affymetrix probes
filtering
probe
MicroarrayData
5 months ago
Fatemeh
• 0
0
votes
1
reply
1.0k
views
filtering on variance
probe
affy
probe
affy
updated 21 months ago by
Gordon Smyth
47k • written 15.2 years ago by
Dennis.Burian@faa.gov
▴ 90
0
votes
0
replies
326
views
Probe Design questions
probe
affy
2.4 years ago
henry1995910343
• 0
4
votes
10
replies
1.4k
views
how to analyze WGCNA results?
cancer
probe
deseq2
annotation
normalization
updated 2.7 years ago by
Kevin Blighe
3.7k • written 2.7 years ago by
rajpal22288
▴ 10
0
votes
8
replies
2.0k
views
Combining 2 datasets from 2 different RNAseq experiments
deseq2
normalization
probe
updated 2.9 years ago by
Michael Love
39k • written 2.9 years ago by
l.s.wijaya
• 0
0
votes
0
replies
264
views
Program to calculate genetic distances with long sequences
probe
go
2.9 years ago
antoniorevail
• 0
0
votes
5
replies
648
views
Does anyone have experience using the massiR package?
massiR
microarray
R
probe
3.4 years ago
Steve Lowe
▴ 10
0
votes
0
replies
297
views
massiR Extracting and Plotting Y Chr Probe Data
probe
microarray
3.4 years ago
Steve Lowe
▴ 10
0
votes
1
reply
511
views
Determining survival correlation among probes
annotation
probe
microarray
3.5 years ago
sbrackett007
• 0
0
votes
4
replies
574
views
Cannot down load the "org.Hs.eg.db" completely
software error
probe
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
1650706262
• 0
2
votes
4
replies
776
views
SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC
probe
normalization
GEOdata
cancer
3.8 years ago
s.goncalvesclaro
▴ 10
0
votes
2
replies
1.2k
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
3.9 years ago
brendan.miller
• 0
1
vote
3
replies
441
views
I can't install the package "matchprobes"
software error
probe
updated 3.9 years ago by
James W. MacDonald
62k • written 3.9 years ago by
1492917006
• 0
0
votes
0
replies
422
views
How to merging multiple GSEs with different GPLs?
microarray
probe
R
4.0 years ago
maryam.sabet
• 0
0
votes
1
reply
759
views
MCLUST: finding the best number of Gaussian components to fit my data
software error
microarray
probe
annotation
updated 4.0 years ago by
Michael Love
39k • written 4.0 years ago by
travascio.andrea91
• 0
0
votes
0
replies
901
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe
affy
probe
affy
updated 4.1 years ago by
Bioconductor Community
0 • written 19.0 years ago by
Matthew Hannah
▴ 940
0
votes
3
replies
3.3k
views
Use probesets with highest baseline expression for differential gene
Annotation
probe
limma
11.0 years ago • updated 4.4 years ago
Gordon Smyth
47k
1
vote
2
replies
580
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays
microarray
probe
statistics
updated 4.4 years ago by
James W. MacDonald
62k • written 4.4 years ago by
ravelarvargas
• 0
0
votes
2
replies
1.5k
views
[ComBat] ComBat outputting NAs with Large Batches - Switch to Log Likelihood
probe
probe
updated 4.9 years ago by
jbloomstein
• 0 • written 10.2 years ago by
Jason Stein
▴ 10
0
votes
0
replies
798
views
Probe annotations for ABI Human Genome Survey V2 microarray using Oracle
annotation
probe
microarray
abi human genome survey v2
Oracle
4.9 years ago
judemtaylor
• 0
1
vote
3
replies
1.6k
views
GO terms: Annotation for HumanMethylation450
Annotation
GO
probe
Annotation
GO
probe
updated 4.9 years ago by
underscore
• 0 • written 9.9 years ago by
Fabrice Tourre
▴ 970
0
votes
1
reply
633
views
index of probes in Illumina Infinium MethylationEPIC BeadChip
probe
5.0 years ago
mcarmel
• 0
4
votes
5
replies
1.7k
views
Retrieving probes mapping to gene ID in microarray analysis
microarray
affymetrix
probeset
probe
updated 5.3 years ago by
Mike Smith
★ 5.9k • written 5.3 years ago by
n.lu
• 0
0
votes
1
reply
909
views
Multiple samples on the same graph
Pathview
probe
updated 5.5 years ago by
Luo Weijun
★ 1.6k • written 5.6 years ago by
Luiz
• 0
0
votes
1
reply
619
views
probe set-gene relation
probe
geneid
probeset
updated 5.8 years ago by
James W. MacDonald
62k • written 5.8 years ago by
basak
• 0
0
votes
8
replies
1.3k
views
raw probe set expression data and masking questions
Normalization
Cancer
probe
affy
PROcess
Normalization
Cancer
probe
affy
PROcess
updated 5.9 years ago by
jacorvar
▴ 40 • written 16.4 years ago by
Schwartz, Donald
▴ 20
1
vote
6
replies
1.2k
views
Remove a list of specific probes from an HTAFeatureSet
pd.clariom.d.human
affy
probe
updated 5.9 years ago by
James W. MacDonald
62k • written 5.9 years ago by
jacorvar
▴ 40
1
vote
5
replies
815
views
Filter out ranges by number of probes
probe
ranges
updated 5.9 years ago by
Mike Smith
★ 5.9k • written 5.9 years ago by
julrodr80
▴ 30
0
votes
0
replies
869
views
removing probes representing in a certain beads
minfi
probe
preprocessing
6.0 years ago
niutster
• 0
0
votes
4
replies
1.5k
views
minfi probe removal
minfi
probe
updated 6.0 years ago by
James W. MacDonald
62k • written 6.0 years ago by
niutster
• 0
3
votes
4
replies
4.4k
views
LIMMA and Agilent single color
Annotation
probe
limma
agilent
12.1 years ago • updated 6.0 years ago
Gordon Smyth
47k
0
votes
1
reply
1.5k
views
LIMMA and Agilent single color
probe
limma
probe
limma
updated 6.1 years ago by
Gordon Smyth
47k • written 12.1 years ago by
De Boever Patrick
▴ 60
1
vote
4
replies
1.6k
views
How to install old GenomicRanges 1.14.4 package ?
bioconductor
R
cancer
probe
deseq2
updated 6.7 years ago by
derbecker
▴ 10 • written 6.7 years ago by
winter_li
• 0
0
votes
1
reply
1.2k
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 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
amans.3008
• 0
0
votes
1
reply
940
views
Importing and Extracting Annotation
annotation
zebrafish
probe
updated 6.8 years ago by
James W. MacDonald
62k • written 6.8 years ago by
atiqahrahman
• 0
2
votes
3
replies
1.4k
views
i need AGI code as my probset
affy
cdf
probe
7.2 years ago • updated 7.0 years ago
Angel
▴ 40
0
votes
5
replies
1.3k
views
"oligo" package: probenames/probeinfo different from expr-set (read.cellfles): miRNA 4.0 (affy)
microarray
probe
annotation
affy
7.0 years ago
dietmar.pils
• 0
0
votes
0
replies
889
views
Help for affy
affy
process
probe
7.0 years ago
weizhong_2007
• 0
0
votes
3
replies
9.8k
views
How to combine expression values of multiple probes for one gene
probe
convert
geneexpression
onechannelgui
updated 7.5 years ago by
svlachavas
▴ 800 • written 7.6 years ago by
ayanava18
▴ 10
1
vote
4
replies
1.0k
views
mutually add a tab in the beggining of the header to make it a valid RMA format
software error
probe
affy
RMA
7.6 years ago
Angel
▴ 40
2
votes
2
replies
2.0k
views
Illumina 450k Annotation Definitions/Articles: How was "Enhancer" status determined?
probe
annotation
illimina 450k methylation
minfi
methylation
7.6 years ago
metamaden
▴ 10
0
votes
5
replies
4.9k
views
How to do Affy ST array analysis
Annotation
Normalization
hgu133a
probe
affy
oligo
Annotation
Normalization
hgu133a
probe
updated 7.7 years ago by
benhrif.oussama
• 0 • written 8.8 years ago by
Guest User
★ 12k
0
votes
1
reply
1.1k
views
simpleaffy segmentation fault
Survival
probe
genefilter
affy
affyio
Survival
probe
genefilter
affy
affyio
updated 7.7 years ago by
vlagani
• 0 • written 16.1 years ago by
Sucheta Tripathy
▴ 170
0
votes
2
replies
891
views
difficulty in mapping gene names to probes coordinates in a celfile
microarray
probe
updated 7.9 years ago by
James W. MacDonald
62k • written 7.9 years ago by
nazaninhoseinkhan
• 0
0
votes
2
replies
1.2k
views
Affymetrix file with probe set id
probe
affy
PROcess
probe
affy
PROcess
updated 7.9 years ago by
nazaninhoseinkhan
• 0 • written 18.3 years ago by
Srinivas Iyyer
▴ 600
0
votes
3
replies
2.1k
views
filtering out probes with no gene symbol from expressionSet
probe
filter
subset
gene symbol
affy
7.9 years ago
alakatos
▴ 120
1
vote
1
reply
1.4k
views
Coercion of MethyLumiSet to MethyLumiR changes raw methylation values?
Normalization
probe
lumi
Normalization
probe
lumi
updated 8.0 years ago by
dsweeney
• 0 • written 8.9 years ago by
Nick Fishbane
▴ 20
1
vote
2
replies
1.4k
views
array quality control, affy probes, contracts setting in limma, result interpretation and weights
limma
affy
probe
qualitycontrol
design and contrast matrix
updated 8.1 years ago by
Gordon Smyth
47k • written 8.1 years ago by
alakatos
▴ 120
6
votes
2
replies
1.4k
views
Should I skip the eBayes step when using Limma for Affymetrix miRNA v1 chip?
miRNA
cdf
probe
limma
miRNA
cdf
probe
limma
updated 8.4 years ago by
Gordon Smyth
47k • written 8.5 years ago by
Guest User
★ 12k
50 results • Page
1 of 1
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Replies
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Guido Hooiveld
★ 3.5k
Also: you could consider using `DABG` for present/absent calls. James elaborated on this in this thread: https://support.bioconductor.org/p…
Comment: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object
by
shaimaa
• 0
I used the combat-seq but the deseq complain as its not integer what should i do
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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