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4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
3
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3
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13k
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How to fix 'long vectors not supported yet' error in R
r
updated 20 days ago by • 0 • written 5.2 years ago by • 0
8
votes
11
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11k
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R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 12 months ago by • 0 • written 6.8 years ago by ▴ 10
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 5 weeks ago by • 0 • written 7.6 years ago by • 0
0
votes
6
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8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler r
updated 3 months ago by ★ 3.9k • written 7.3 years ago by • 0
22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 5 months ago by ▴ 10 • written 2.0 years ago by ▴ 50
7
votes
5
replies
6.8k
views
biomaRt server error, and mirrors do not help
ensembl biomaRt R
updated 6 months ago by • 0 • written 24 months ago by ▴ 40
10
votes
10
replies
6.6k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 4 weeks ago by • 0 • written 5 months ago by ▴ 10
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
2
votes
4
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3.8k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 10 weeks ago by 50k • written 4.7 years ago by • 0
1
vote
12
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2.3k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 3 months ago by • 0 • written 2.5 years ago by ▴ 380
1
vote
5
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2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo microarray r bioconductor
written 9.2 years ago by ▴ 10
4
votes
8
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2.1k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 16 months ago by ▴ 20
0
votes
2
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2.0k
views
Creating a qPCRset object from a text file
qPCRset object nondetects r package txt
updated 6 months ago by • 0 • written 6.3 years ago by • 0
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R GillespieColin ArrayExpress import TimeSeriesExperiment
updated 6 months ago by ▴ 40 • written 18 months ago by ▴ 20
1
vote
3
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1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.1k • written 6.6 years ago by • 0
0
votes
3
replies
1.6k
views
Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
R oligoClasses Oligoclass Bioconductor Oligo
written 3.2 years ago by • 0
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 11 months ago by • 0 • written 5.5 years ago by • 0
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR Methylation R Gviz
updated 5 months ago by ▴ 730 • written 3.0 years ago by • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata ChAMPdata champload R ChAMP
updated 10 months ago by • 0 • written 3.2 years ago by • 0
0
votes
10
replies
790
views
Unable to locate BioMart dataset for Dog10K_Boxer_Tasha
R BioMart biomaRt
5 months ago • updated 7 weeks ago ScafioRuo • 0
0
votes
1
reply
620
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 11 months ago by 50k • written 11 months ago by • 0
1
vote
2
replies
587
views
biomaRt not retrieving complete list of functional consequences associated with list of SNPs
ensembl R biomaRt
9 months ago Miguel • 0
0
votes
2
replies
541
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago • updated 7 months ago yr542 • 0
3
votes
4
replies
516
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
5 months ago pl23 • 0
0
votes
1
reply
505
views
Gene enrichment analysis
analysis R GOfuncR
updated 10 months ago by ▴ 730 • written 10 months ago by • 0
0
votes
1
reply
489
views
DEseq2 Single cell data paired design
R
updated 12 months ago by ▴ 30 • written 12 months ago by • 0
0
votes
3
replies
469
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
4
replies
336
views
limma with interaction term
R biostatistics limma Epigenetics
10 weeks ago • updated 8 weeks ago Jitendra ▴ 10
0
votes
0
replies
214
views
multipollutant models
statistics Regression r limma
4 months ago Jitendra ▴ 10
0
votes
0
replies
108
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
7 weeks ago danalvoronov ▴ 10
32 results • Page 1 of 1
Recent ...
Replies
Comment: get BM error by Fara • 0
Thank you for the reply. The examples are these. ENSGACG00000014473 ENSGACG00000015168 ENSGACG00000007529
Comment: get BM error by Mike Smith ★ 6.5k
Can you provide an example of the Ensemble IDs you're trying to convert?
Comment: How to retrieve gene ontology GO class? by bandconductor • 0
Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence. I have …
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Votes
Comment: get BM error
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
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