Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
geo
•
reset
1
vote
10
replies
404
views
Obtaining pheno data from CEL files
GEO
affy
22 days ago • updated 16 days ago
Kurtis
• 0
0
votes
1
reply
520
views
how to solve this error
DESeq2
GEO
miRNAData
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
ashisaanz
• 0
1
vote
5
replies
1.1k
views
Can't read in CEL files
GEO
GEOquery
22 months ago
OE
• 0
5
votes
7
replies
2.1k
views
GEO series matrix empty
GEOquery
GEO
2.2 years ago
gs.123
▴ 20
1
vote
2
replies
2.4k
views
GEO RNASeq data query
GEOquery
RNASeq
GEO
updated 2.4 years ago by
Sean Davis
21k • written 2.4 years ago by
20yx17
▴ 10
6
votes
7
replies
2.2k
views
GEOquery reading error on Windows.
GEOquery
GEO
Gene
updated 2.5 years ago by
James W. MacDonald
65k • written 2.5 years ago by
Caitlin
▴ 50
1
vote
3
replies
1.1k
views
Microarray - Illumina Metadata
limma
GEO
MicroarrayData
affy
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
RMP87
• 0
6
votes
5
replies
1.2k
views
a problem of package ""
GEO
GEOquery
updated 2.9 years ago by
Hervé Pagès
16k • written 2.9 years ago by
sheldon19931016
▴ 20
2
votes
3
replies
980
views
Problem about Geoquery
GEO
GEOquery
2.9 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
3.1 years ago
hgalmoore
• 0
2
votes
1
reply
2.8k
views
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"ExpressionSet"’
GEO
oligo
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
Gero
• 0
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
H. Z. Amini
▴ 10
0
votes
0
replies
714
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 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
andrej.stoll.de
▴ 10
1
vote
1
reply
1.1k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
lsbew
• 0
0
votes
1
reply
1.1k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
Guillaume Robert
• 0
1
vote
4
replies
1.2k
views
How to obtain the two gene expression datasets from a dual channel GEO dataset?
dual-channel
GEO
gene-expression
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
davide.chicco
• 0
4
votes
5
replies
1.4k
views
All genes display positive fold change in topTable results after limma
limma
microarray
foldchange
DEG
GEO
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
Pietro
▴ 40
0
votes
2
replies
871
views
Annotation Using GEOquery
Annotation
GEO
TXT
updated 4.5 years ago by
Sean Davis
21k • written 4.5 years ago by
ekl
• 0
0
votes
6
replies
1.3k
views
Opening Illumina HT12 V3.0 Data from GEO
limma
normalization
GEO
4.6 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 4.9 years ago by
Mike Smith
★ 6.5k • written 4.9 years ago by
wes
▴ 10
0
votes
0
replies
946
views
GEOquery: series matrix not parsing correctly
GEOquery
GEO
updated 5.0 years ago by
James W. MacDonald
65k • written 5.0 years ago by
andy_shaps
▴ 10
3
votes
6
replies
2.9k
views
GEOquery: HTTP error 403
GEOquery
GEO
HTTP error 403
5.0 years ago
andy_shaps
▴ 10
5
votes
12
replies
2.6k
views
Using eset while parsing GSE file located in a path
GEO
geoquery
updated 5.7 years ago by
Sean Davis
21k • written 5.7 years ago by
mahm
▴ 20
1
vote
3
replies
924
views
Filtering the expression values of a gene from GEO
GEO
microarray
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
mahm
▴ 20
2
votes
6
replies
1.4k
views
error reading GSE using getGEO()
r
geo
getgeo
5.8 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 5.8 years ago by
Sean Davis
21k • written 5.8 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 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
Harpreet Kaur
• 0
0
votes
4
replies
1.5k
views
GEOquery using keywords in R
GEO
geoquery
geometadb
updated 5.9 years ago by
Sean Davis
21k • written 5.9 years ago by
Didi
▴ 10
0
votes
0
replies
1.1k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO
minfi
5.9 years ago
daniel.green
• 0
1
vote
1
reply
1.3k
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 6.3 years ago by
Sean Davis
21k • written 7.0 years ago by
jblack29
• 0
3
votes
5
replies
4.9k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
6.3 years ago
martinguerrerog89
▴ 20
10
votes
7
replies
2.4k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery
summarizedexperiment
GEO
matrix
updated 6.3 years ago by
Sean Davis
21k • written 6.3 years ago by
rbronste
▴ 60
1
vote
3
replies
2.4k
views
Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi
geoquery
geo
illumina human ht-12 v4
gene expression
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 years ago by
aaronrosenstein
• 0
0
votes
1
reply
1.4k
views
GEOquery download error
geoquery error message
GEOquery
GSE
GEO
6.7 years ago
Barah
▴ 20
1
vote
3
replies
1.4k
views
Getting gene annotation for a GEO dataset
geo
6.8 years ago
yuvallb
• 0
2
votes
2
replies
2.1k
views
GEOquery error in downloading SOFT files
geoquery
getgeo
GEO
7.4 years ago
hzc363
▴ 20
0
votes
1
reply
2.1k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
akridgerunner
▴ 30
2
votes
4
replies
1.6k
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 8.3 years ago by
Mike Smith
★ 6.5k • written 8.3 years ago by
maedakus
▴ 10
0
votes
5
replies
1.9k
views
collect an expression dataset
limma
CEL
GEO
affydata
expresiondataset
updated 8.4 years ago by
Robert Castelo
★ 3.3k • written 8.4 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 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
mamillerpa
• 0
46 results • Page
1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Awards
• All
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Locations
• All
France,
just now
United Kingdom,
just now
France,
7 minutes ago
UPF, Barcelona, Spain,
17 minutes ago
Germany,
19 minutes ago
Traffic: 845 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6