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geo
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0
votes
1
reply
59
views
how to solve this error
DESeq2
GEO
miRNAData
updated 7 days ago by
ATpoint
★ 2.9k • written 7 days ago by
ashisaanz
• 0
1
vote
5
replies
487
views
Can't read in CEL files
GEO
GEOquery
11 months ago
OE
• 0
5
votes
7
replies
1.3k
views
GEO series matrix empty
GEOquery
GEO
15 months ago
gs.123
▴ 20
1
vote
2
replies
1.4k
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 18 months ago by
Sean Davis
21k • written 18 months ago by
20yx17
▴ 10
6
votes
7
replies
1.4k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 18 months ago by
James W. MacDonald
63k • written 18 months ago by
Caitlin
▴ 50
1
vote
3
replies
719
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 20 months ago by
James W. MacDonald
63k • written 20 months ago by
RMP87
• 0
6
votes
5
replies
810
views
a problem of package ""
GEO
GEOquery
updated 2.0 years ago by
Hervé Pagès
16k • written 2.0 years ago by
sheldon19931016
▴ 20
2
votes
3
replies
586
views
Problem about Geoquery
GEO
GEOquery
2.0 years ago
sheldon19931016
▴ 20
4
votes
2
replies
883
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 2.1 years ago by
James W. MacDonald
63k • written 2.1 years ago by
Gero
• 0
3
votes
4
replies
965
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
2.2 years ago
hgalmoore
• 0
2
votes
1
reply
1.8k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO
oligo
updated 2.2 years ago by
James W. MacDonald
63k • written 2.2 years ago by
Gero
• 0
5
votes
5
replies
1.7k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 2.3 years ago by
James W. MacDonald
63k • written 2.3 years ago by
H. Z. Amini
• 0
0
votes
0
replies
457
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER
TCGA
GEO
2.7 years ago
andrade4beatriz
• 0
2
votes
2
replies
1.0k
views
How to Analyse Datasets from GEO
geo
rnaseq
deseq2
tpm
updated 3.1 years ago by
Kevin Blighe
3.8k • written 3.1 years ago by
andrej.stoll.de
▴ 10
1
vote
1
reply
743
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 3.1 years ago by
Robert Castelo
★ 3.0k • written 3.1 years ago by
lsbew
• 0
0
votes
1
reply
668
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 3.2 years ago by
James W. MacDonald
63k • written 3.2 years ago by
Guillaume Robert
• 0
1
vote
4
replies
739
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel
GEO
gene-expression
updated 3.3 years ago by
Gordon Smyth
47k • written 3.3 years ago by
davide.chicco
• 0
4
votes
5
replies
917
views
All genes display positive fold change in topTable results after limma
limma
microarray
foldchange
DEG
GEO
updated 3.3 years ago by
Gordon Smyth
47k • written 3.3 years ago by
Pietro
▴ 40
0
votes
2
replies
583
views
Annotation Using GEOquery
Annotation
GEO
TXT
updated 3.6 years ago by
Sean Davis
21k • written 3.6 years ago by
ekl
• 0
0
votes
6
replies
912
views
Opening Illumina HT12 V3.0 Data from GEO
limma
normalization
GEO
3.7 years ago
FL512
• 0
3
votes
2
replies
814
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart
geo
software error
ensembl
updated 4.0 years ago by
Mike Smith
★ 6.0k • written 4.0 years ago by
wes
▴ 10
0
votes
0
replies
689
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 4.1 years ago by
James W. MacDonald
63k • written 4.1 years ago by
andy_shaps
▴ 10
3
votes
6
replies
2.3k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
4.1 years ago
andy_shaps
▴ 10
5
votes
12
replies
2.0k
views
Using eset while parsing GSE file located in a path
GEO
geoquery
updated 4.8 years ago by
Sean Davis
21k • written 4.8 years ago by
mahm
▴ 20
1
vote
3
replies
698
views
Filtering the expression values of a gene from GEO
GEO
microarray
updated 4.8 years ago by
James W. MacDonald
63k • written 4.8 years ago by
mahm
▴ 20
2
votes
6
replies
974
views
error reading GSE using getGEO()
r
geo
getgeo
4.9 years ago
jaleh.amo
• 0
3
votes
2
replies
990
views
Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
geometadb
GEO
R
bioconductor
updated 4.9 years ago by
Sean Davis
21k • written 4.9 years ago by
gaby8638
▴ 20
1
vote
2
replies
1.4k
views
Targets.txt file missing in agilent GEO data. How do I preprocess raw Agilent file of GEO data or how to makethe expression matrix step by step from …
limma
microarray
agilent microarrays
GEO
updated 5.0 years ago by
James W. MacDonald
63k • written 5.0 years ago by
hks04180
• 0
0
votes
4
replies
1.1k
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 5.0 years ago by
Sean Davis
21k • written 5.0 years ago by
Didi
▴ 10
0
votes
0
replies
749
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO
minfi
5.0 years ago
daniel.green
• 0
1
vote
1
reply
904
views
GEOquery: Diagnosing SOFT file error
geoquery
geo data
geo
soft files
updated 5.2 years ago by
Sean Davis
21k • written 5.2 years ago by
supermanrocketboy
▴ 10
3
votes
11
replies
3.1k
views
GEOquery http:// url error
geoquery
error
getgeo
microarray
geo
updated 5.4 years ago by
Sean Davis
21k • written 6.1 years ago by
jblack29
• 0
3
votes
5
replies
3.8k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
5.4 years ago
martinguerrerog89
▴ 20
10
votes
7
replies
1.8k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery
summarizedexperiment
GEO
matrix
updated 5.4 years ago by
Sean Davis
21k • written 5.4 years ago by
rbronste
▴ 60
1
vote
3
replies
1.9k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi
geoquery
geo
illumina human ht-12 v4
gene expression
updated 5.6 years ago by
Gordon Smyth
47k • written 5.6 years ago by
aaronrosenstein
• 0
0
votes
1
reply
1.2k
views
GEOquery download error
geoquery error message
GEOquery
GSE
GEO
5.8 years ago
Barah
▴ 20
1
vote
3
replies
1.1k
views
Getting gene annotation for a GEO dataset
geo
5.9 years ago
yuvallb
• 0
2
votes
2
replies
1.6k
views
GEOquery error in downloading SOFT files
geoquery
getgeo
GEO
6.5 years ago
hzc363
▴ 20
0
votes
1
reply
1.7k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 7.0 years ago by
Gordon Smyth
47k • written 7.0 years ago by
akridgerunner
▴ 30
2
votes
4
replies
1.2k
views
read bead-level data directly by lumi
bead-level
GEO
lumi
updated 7.2 years ago by
Mike Smith
★ 6.0k • written 7.2 years ago by
gnilihzeux
• 0
1
vote
2
replies
1.1k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 7.2 years ago by
Mike Smith
★ 6.0k • written 7.2 years ago by
gnilihzeux
• 0
0
votes
1
reply
855
views
data handling from GSE22216 to exprSet object
GEO
updated 7.4 years ago by
Mike Smith
★ 6.0k • written 7.4 years ago by
maedakus
▴ 10
0
votes
5
replies
1.5k
views
collect an expression dataset
limma
CEL
GEO
affydata
expresiondataset
updated 7.5 years ago by
Robert Castelo
★ 3.0k • written 7.5 years ago by
libya.tahani
• 0
0
votes
1
reply
945
views
Getting data from GEO
affymetrix microarrays
GEO
geoquery
updated 7.5 years ago by
James W. MacDonald
63k • written 7.5 years ago by
libya.tahani
• 0
5
votes
7
replies
1.6k
views
what conditions affect my gene (with limma?)
limma
geo
experimental design
updated 7.8 years ago by
Gordon Smyth
47k • written 7.8 years ago by
mamillerpa
• 0
45 results • Page
1 of 1
Recent ...
Replies
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network
by
andres.firrincieli
▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa
by
Jean-Philippe Fortin
• 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed
by
Emile
• 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values
by
Laurent Gatto
1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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