Showing : GEO • reset
0
votes
3
replies
557
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
5 months ago gallantk5 • 0
0
votes
4
replies
660
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery GEO TSV
updated 5 months ago by 21k • written 5 months ago by • 0
0
votes
9
replies
767
views
Research Project - Expanding search funtionality on the GEO database
GEOquery GEO
6 months ago • updated 5 months ago gallantk5 • 0
1
vote
10
replies
1.0k
views
Obtaining pheno data from CEL files
GEO affy
8 months ago Kurtis • 0
0
votes
1
reply
756
views
how to solve this error
DESeq2 GEO miRNAData
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
1
vote
5
replies
1.4k
views
Can't read in CEL files
GEO GEOquery
2.5 years ago OE • 0
5
votes
7
replies
2.7k
views
GEO series matrix empty
GEOquery GEO
2.8 years ago gs.123 ▴ 20
1
vote
2
replies
2.9k
views
GEO RNASeq data query
GEOquery RNASeq GEO
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 10
6
votes
7
replies
2.7k
views
GEOquery reading error on Windows.
GEOquery GEO Gene
updated 3.1 years ago by 67k • written 3.1 years ago by ▴ 50
1
vote
3
replies
1.4k
views
Microarray - Illumina Metadata
limma GEO MicroarrayData affy
updated 3.2 years ago by 67k • written 3.2 years ago by • 0
6
votes
5
replies
1.5k
views
a problem of package ""
GEO GEOquery
updated 3.6 years ago by 16k • written 3.6 years ago by ▴ 20
2
votes
3
replies
1.3k
views
Problem about Geoquery
GEO GEOquery
3.6 years ago sheldon19931016 ▴ 20
4
votes
2
replies
1.5k
views
TargetsFile. Where it is?
Limma ArrayExpress GEO
updated 3.7 years ago by 67k • written 3.7 years ago by • 0
3
votes
4
replies
1.7k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.7 years ago hgalmoore • 0
2
votes
1
reply
3.4k
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 67k • written 3.7 years ago by • 0
5
votes
5
replies
3.2k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.8 years ago by 67k • written 3.8 years ago by ▴ 10
0
votes
0
replies
913
views
Identify significantly different DNA methylation probes in tumor and normal samples GBM ELMER R package
ELMER TCGA GEO
4.3 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 ★ 4.0k • written 4.6 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Table expression data from GEO file
GEO expression GEOquery
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by • 0
0
votes
1
reply
1.5k
views
get Gene ID from GEO microarray dataset with fData
GEO
updated 4.8 years ago by 67k • written 4.8 years ago by • 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 4.9 years ago by 52k • written 4.9 years ago by • 0
4
votes
5
replies
1.7k
views
All genes display positive fold change in topTable results after limma
limma microarray foldchange DEG GEO
updated 4.9 years ago by 52k • written 4.9 years ago by ▴ 40
0
votes
2
replies
1.1k
views
Annotation Using GEOquery
Annotation GEO TXT
updated 5.1 years ago by 21k • written 5.1 years ago by • 0
0
votes
6
replies
1.6k
views
Opening Illumina HT12 V3.0 Data from GEO
limma normalization GEO
5.2 years ago FL512 • 0
3
votes
2
replies
1.4k
views
GEO Download - "The query to BioMart webservice returned an invalid result..."
biomart geo software error ensembl
updated 5.5 years ago by ★ 6.6k • written 5.5 years ago by ▴ 10
0
votes
0
replies
1.1k
views
GEOquery: series matrix not parsing correctly
GEOquery GEO
updated 5.6 years ago by 67k • written 5.6 years ago by ▴ 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
3.0k
views
Using eset while parsing GSE file located in a path
GEO geoquery
updated 6.3 years ago by 21k • written 6.3 years ago by ▴ 20
1
vote
3
replies
1.1k
views
Filtering the expression values of a gene from GEO
GEO microarray
updated 6.4 years ago by 67k • written 6.4 years ago by ▴ 20
2
votes
6
replies
1.8k
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 21k • written 6.5 years ago by ▴ 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 67k • written 6.5 years ago by • 0
0
votes
4
replies
1.8k
views
GEOquery using keywords in R
GEO geoquery geometadb
updated 6.6 years ago by 21k • written 6.6 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Preprocessing and Normalisation of GEO Meth/Unmeth signals
GEO minfi
6.6 years ago daniel.green • 0
1
vote
1
reply
1.5k
views
GEOquery: Diagnosing SOFT file error
geoquery geo data geo soft files
updated 6.8 years ago by 21k • written 6.8 years ago by ▴ 10
3
votes
11
replies
4.5k
views
GEOquery http:// url error
geoquery error getgeo microarray geo
updated 6.9 years ago by 21k • written 7.7 years ago by • 0
3
votes
5
replies
5.7k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
6.9 years ago martinguerrerog89 ▴ 20
10
votes
7
replies
2.8k
views
SummarizedExperiment object from GEOquery obtained GSE
geoquery summarizedexperiment GEO matrix
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 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 7.2 years ago by 52k • written 7.2 years ago by • 0
0
votes
1
reply
1.7k
views
GEOquery download error
geoquery error message GEOquery GSE GEO
7.3 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
8.1 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 52k • written 8.5 years ago by ▴ 30
2
votes
4
replies
1.8k
views
read bead-level data directly by lumi
bead-level GEO lumi
updated 8.8 years ago by ★ 6.6k • written 8.8 years ago by • 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 8.8 years ago by ★ 6.6k • written 8.8 years ago by • 0
0
votes
1
reply
1.2k
views
data handling from GSE22216 to exprSet object
GEO
updated 8.9 years ago by ★ 6.6k • written 8.9 years ago by ▴ 10
0
votes
5
replies
2.1k
views
collect an expression dataset
limma CEL GEO affydata expresiondataset
updated 9.1 years ago by ★ 3.4k • written 9.1 years ago by • 0
0
votes
1
reply
1.4k
views
Getting data from GEO
affymetrix microarrays GEO geoquery
updated 9.1 years ago by 67k • written 9.1 years ago by • 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 52k • written 9.3 years ago by • 0
49 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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