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Showing :
geo
•
reset
0
votes
3
replies
525
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
4 months ago
gallantk5
• 0
0
votes
4
replies
605
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery
GEO
TSV
updated 4 months ago by
Sean Davis
21k • written 4 months ago by
gallantk5
• 0
0
votes
9
replies
715
views
Research Project - Expanding search funtionality on the GEO database
GEOquery
GEO
5 months ago • updated 4 months ago
gallantk5
• 0
1
vote
10
replies
935
views
Obtaining pheno data from CEL files
GEO
affy
7 months ago
Kurtis
• 0
0
votes
1
reply
732
views
how to solve this error
DESeq2
GEO
miRNAData
updated 18 months ago by
ATpoint
★ 4.5k • written 18 months ago by
ashisaanz
• 0
1
vote
5
replies
1.4k
views
Can't read in CEL files
GEO
GEOquery
2.4 years ago
OE
• 0
5
votes
7
replies
2.6k
views
GEO series matrix empty
GEOquery
GEO
2.8 years ago • updated 2.7 years ago
gs.123
▴ 20
1
vote
2
replies
2.8k
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 3.0 years ago by
Sean Davis
21k • written 3.0 years ago by
20yx17
▴ 10
6
votes
7
replies
2.7k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 3.0 years ago by
James W. MacDonald
67k • written 3.0 years ago by
Caitlin
▴ 50
1
vote
3
replies
1.4k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
RMP87
• 0
6
votes
5
replies
1.5k
views
a problem of package ""
GEO
GEOquery
updated 3.5 years ago by
Hervé Pagès
16k • written 3.5 years ago by
sheldon19931016
▴ 20
2
votes
3
replies
1.3k
views
Problem about Geoquery
GEO
GEOquery
3.5 years ago
sheldon19931016
▴ 20
4
votes
2
replies
1.5k
views
TargetsFile. Where it is?
Limma
ArrayExpress
GEO
updated 3.6 years ago by
James W. MacDonald
67k • written 3.6 years ago by
Gero
• 0
3
votes
4
replies
1.7k
views
GEO + RNA-seq. Total Newbie.
RNASeqData
RNASeq
GEO
RNASeqR
HELP
3.6 years ago
hgalmoore
• 0
2
votes
1
reply
3.3k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO
oligo
updated 3.7 years ago by
James W. MacDonald
67k • written 3.7 years ago by
Gero
• 0
5
votes
5
replies
3.1k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.8 years ago by
James W. MacDonald
67k • written 3.8 years ago by
H. Z. Amini
▴ 10
0
votes
0
replies
900
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER
TCGA
GEO
4.2 years ago
andrade4beatriz
• 0
2
votes
2
replies
2.1k
views
How to Analyse Datasets from GEO
geo
rnaseq
deseq2
tpm
updated 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 years ago by
andrej.stoll.de
▴ 10
1
vote
1
reply
1.3k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 4.6 years ago by
Robert Castelo
★ 3.4k • written 4.6 years ago by
lsbew
• 0
0
votes
1
reply
1.5k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 4.7 years ago by
James W. MacDonald
67k • written 4.7 years ago by
Guillaume Robert
• 0
1
vote
4
replies
1.4k
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel
GEO
gene-expression
updated 4.8 years ago by
Gordon Smyth
51k • written 4.8 years ago by
davide.chicco
• 0
4
votes
5
replies
1.6k
views
All genes display positive fold change in topTable results after limma
limma
microarray
foldchange
DEG
GEO
updated 4.8 years ago by
Gordon Smyth
51k • written 4.8 years ago by
Pietro
▴ 40
0
votes
2
replies
1.1k
views
Annotation Using GEOquery
Annotation
GEO
TXT
updated 5.0 years ago by
Sean Davis
21k • written 5.0 years ago by
ekl
• 0
0
votes
6
replies
1.5k
views
Opening Illumina HT12 V3.0 Data from GEO
limma
normalization
GEO
5.1 years ago
FL512
• 0
3
votes
2
replies
1.3k
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart
geo
software error
ensembl
updated 5.5 years ago by
Mike Smith
★ 6.6k • written 5.5 years ago by
wes
▴ 10
0
votes
0
replies
1.1k
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 5.5 years ago by
James W. MacDonald
67k • written 5.5 years ago by
andy_shaps
▴ 10
3
votes
6
replies
3.5k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
5.6 years ago
andy_shaps
▴ 10
5
votes
12
replies
2.9k
views
Using eset while parsing GSE file located in a path
GEO
geoquery
updated 6.2 years ago by
Sean Davis
21k • written 6.2 years ago by
mahm
▴ 20
1
vote
3
replies
1.1k
views
Filtering the expression values of a gene from GEO
GEO
microarray
updated 6.3 years ago by
James W. MacDonald
67k • written 6.3 years ago by
mahm
▴ 20
2
votes
6
replies
1.7k
views
error reading GSE using getGEO()
r
geo
getgeo
6.4 years ago
jaleh.amo
• 0
3
votes
2
replies
1.6k
views
Unable to connect to 'watson.nci.nih.gov' on port 80 using GEOmetadb R library
geometadb
GEO
R
bioconductor
updated 6.4 years ago by
Sean Davis
21k • written 6.4 years ago by
gaby8638
▴ 20
1
vote
2
replies
1.9k
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 6.5 years ago by
James W. MacDonald
67k • written 6.5 years ago by
Harpreet Kaur
• 0
0
votes
4
replies
1.7k
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 6.5 years ago by
Sean Davis
21k • written 6.5 years ago by
Didi
▴ 10
0
votes
0
replies
1.2k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO
minfi
6.5 years ago
daniel.green
• 0
1
vote
1
reply
1.5k
views
GEOquery: Diagnosing SOFT file error
geoquery
geo data
geo
soft files
updated 6.7 years ago by
Sean Davis
21k • written 6.7 years ago by
supermanrocketboy
▴ 10
3
votes
11
replies
4.5k
views
GEOquery http:// url error
geoquery
error
getgeo
microarray
geo
updated 6.8 years ago by
Sean Davis
21k • written 7.6 years ago by
jblack29
• 0
3
votes
5
replies
5.6k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
6.8 years ago
martinguerrerog89
▴ 20
10
votes
7
replies
2.8k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery
summarizedexperiment
GEO
matrix
updated 6.9 years ago by
Sean Davis
21k • written 6.9 years ago by
rbronste
▴ 60
1
vote
3
replies
2.7k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi
geoquery
geo
illumina human ht-12 v4
gene expression
updated 7.1 years ago by
Gordon Smyth
51k • written 7.1 years ago by
aaronrosenstein
• 0
0
votes
1
reply
1.6k
views
GEOquery download error
geoquery error message
GEOquery
GSE
GEO
7.2 years ago
Barah
▴ 20
1
vote
3
replies
1.7k
views
Getting gene annotation for a GEO dataset
geo
7.4 years ago
yuvallb
• 0
2
votes
2
replies
2.5k
views
GEOquery error in downloading SOFT files
geoquery
getgeo
GEO
8.0 years ago
hzc363
▴ 20
0
votes
1
reply
2.4k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 8.5 years ago by
Gordon Smyth
51k • written 8.5 years ago by
akridgerunner
▴ 30
2
votes
4
replies
1.8k
views
read bead-level data directly by lumi
bead-level
GEO
lumi
updated 8.7 years ago by
Mike Smith
★ 6.6k • written 8.7 years ago by
gnilihzeux
• 0
1
vote
2
replies
1.6k
views
readIllumina couln't read bead-level txt file from GEO raw data
beadarray
bead-level
GEO
lumi
updated 8.7 years ago by
Mike Smith
★ 6.6k • written 8.7 years ago by
gnilihzeux
• 0
0
votes
1
reply
1.2k
views
data handling from GSE22216 to exprSet object
GEO
updated 8.9 years ago by
Mike Smith
★ 6.6k • written 8.9 years ago by
maedakus
▴ 10
0
votes
5
replies
2.1k
views
collect an expression dataset
limma
CEL
GEO
affydata
expresiondataset
updated 9.0 years ago by
Robert Castelo
★ 3.4k • written 9.0 years ago by
libya.tahani
• 0
0
votes
1
reply
1.4k
views
Getting data from GEO
affymetrix microarrays
GEO
geoquery
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
libya.tahani
• 0
5
votes
7
replies
2.3k
views
what conditions affect my gene (with limma?)
limma
geo
experimental design
updated 9.3 years ago by
Gordon Smyth
51k • written 9.3 years ago by
mamillerpa
• 0
49 results • Page
1 of 1
Recent ...
Replies
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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