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geo
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0
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1
reply
481
views
how to solve this error
DESeq2
GEO
miRNAData
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
ashisaanz
• 0
1
vote
5
replies
1.0k
views
Can't read in CEL files
GEO
GEOquery
21 months ago
OE
• 0
5
votes
7
replies
2.0k
views
GEO series matrix empty
GEOquery
GEO
2.1 years ago
gs.123
▴ 20
1
vote
2
replies
2.3k
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 2.3 years ago by
Sean Davis
21k • written 2.3 years ago by
20yx17
▴ 10
6
votes
7
replies
2.1k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 2.4 years ago by
James W. MacDonald
65k • written 2.4 years ago by
Caitlin
▴ 50
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
RMP87
• 0
6
votes
5
replies
1.2k
views
a problem of package ""
GEO
GEOquery
updated 2.8 years ago by
Hervé Pagès
16k • written 2.8 years ago by
sheldon19931016
▴ 20
2
votes
3
replies
949
views
Problem about Geoquery
GEO
GEOquery
2.8 years ago
sheldon19931016
▴ 20
4
votes
2
replies
1.3k
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Gero
• 0
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.0 years ago
hgalmoore
• 0
2
votes
1
reply
2.7k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO
oligo
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
Gero
• 0
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
H. Z. Amini
▴ 10
0
votes
0
replies
697
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER
TCGA
GEO
3.6 years ago
andrade4beatriz
• 0
2
votes
2
replies
1.5k
views
How to Analyse Datasets from GEO
geo
rnaseq
deseq2
tpm
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
andrej.stoll.de
▴ 10
1
vote
1
reply
1.0k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 3.9 years ago by
Robert Castelo
★ 3.1k • written 3.9 years ago by
lsbew
• 0
0
votes
1
reply
1.1k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Guillaume Robert
• 0
1
vote
4
replies
1.1k
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel
GEO
gene-expression
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
davide.chicco
• 0
4
votes
5
replies
1.3k
views
All genes display positive fold change in topTable results after limma
limma
microarray
foldchange
DEG
GEO
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
Pietro
▴ 40
0
votes
2
replies
852
views
Annotation Using GEOquery
Annotation
GEO
TXT
updated 4.4 years ago by
Sean Davis
21k • written 4.4 years ago by
ekl
• 0
0
votes
6
replies
1.3k
views
Opening Illumina HT12 V3.0 Data from GEO
limma
normalization
GEO
4.5 years ago
FL512
• 0
3
votes
2
replies
1.1k
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart
geo
software error
ensembl
updated 4.8 years ago by
Mike Smith
★ 6.5k • written 4.8 years ago by
wes
▴ 10
0
votes
0
replies
924
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
andy_shaps
▴ 10
3
votes
6
replies
2.8k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
4.9 years ago
andy_shaps
▴ 10
5
votes
12
replies
2.5k
views
Using eset while parsing GSE file located in a path
GEO
geoquery
updated 5.6 years ago by
Sean Davis
21k • written 5.6 years ago by
mahm
▴ 20
1
vote
3
replies
905
views
Filtering the expression values of a gene from GEO
GEO
microarray
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
mahm
▴ 20
2
votes
6
replies
1.4k
views
error reading GSE using getGEO()
r
geo
getgeo
5.7 years ago
jaleh.amo
• 0
3
votes
2
replies
1.3k
views
Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
geometadb
GEO
R
bioconductor
updated 5.7 years ago by
Sean Davis
21k • written 5.7 years ago by
gaby8638
▴ 20
1
vote
2
replies
1.7k
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 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
hks04180
• 0
0
votes
4
replies
1.4k
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 5.8 years ago by
Sean Davis
21k • written 5.8 years ago by
Didi
▴ 10
0
votes
0
replies
1.0k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO
minfi
5.8 years ago
daniel.green
• 0
1
vote
1
reply
1.2k
views
GEOquery: Diagnosing SOFT file error
geoquery
geo data
geo
soft files
updated 6.1 years ago by
Sean Davis
21k • written 6.1 years ago by
supermanrocketboy
▴ 10
3
votes
11
replies
3.9k
views
GEOquery http:// url error
geoquery
error
getgeo
microarray
geo
updated 6.2 years ago by
Sean Davis
21k • written 7.0 years ago by
jblack29
• 0
3
votes
5
replies
4.8k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
6.2 years ago
martinguerrerog89
▴ 20
10
votes
7
replies
2.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery
summarizedexperiment
GEO
matrix
updated 6.2 years ago by
Sean Davis
21k • written 6.2 years ago by
rbronste
▴ 60
1
vote
3
replies
2.3k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi
geoquery
geo
illumina human ht-12 v4
gene expression
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
aaronrosenstein
• 0
0
votes
1
reply
1.4k
views
GEOquery download error
geoquery error message
GEOquery
GSE
GEO
6.6 years ago
Barah
▴ 20
1
vote
3
replies
1.4k
views
Getting gene annotation for a GEO dataset
geo
6.7 years ago
yuvallb
• 0
2
votes
2
replies
2.0k
views
GEOquery error in downloading SOFT files
geoquery
getgeo
GEO
7.3 years ago
hzc363
▴ 20
0
votes
1
reply
2.1k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
akridgerunner
▴ 30
2
votes
4
replies
1.5k
views
read bead-level data directly by lumi
bead-level
GEO
lumi
updated 8.1 years ago by
Mike Smith
★ 6.5k • written 8.1 years ago by
gnilihzeux
• 0
1
vote
2
replies
1.4k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 8.1 years ago by
Mike Smith
★ 6.5k • written 8.1 years ago by
gnilihzeux
• 0
0
votes
1
reply
1.1k
views
data handling from GSE22216 to exprSet object
GEO
updated 8.2 years ago by
Mike Smith
★ 6.5k • written 8.2 years ago by
maedakus
▴ 10
0
votes
5
replies
1.8k
views
collect an expression dataset
limma
CEL
GEO
affydata
expresiondataset
updated 8.3 years ago by
Robert Castelo
★ 3.1k • written 8.3 years ago by
libya.tahani
• 0
0
votes
1
reply
1.2k
views
Getting data from GEO
affymetrix microarrays
GEO
geoquery
updated 8.4 years ago by
James W. MacDonald
65k • written 8.4 years ago by
libya.tahani
• 0
5
votes
7
replies
2.0k
views
what conditions affect my gene (with limma?)
limma
geo
experimental design
updated 8.6 years ago by
Gordon Smyth
50k • written 8.6 years ago by
mamillerpa
• 0
45 results • Page
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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James W. MacDonald
65k
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