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22
votes
15
replies
7.4k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt
RNASeqData
R
updated 5 months ago by
Marie
▴ 10 • written 2.0 years ago by
Dina
▴ 50
10
votes
10
replies
6.6k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 4 weeks ago by
juo5
• 0 • written 6 months ago by
Abhishek
▴ 10
8
votes
11
replies
11k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5
r
hdf5
updated 12 months ago by
Yijing
• 0 • written 6.8 years ago by
him4u324
▴ 10
7
votes
5
replies
6.8k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 6 months ago by
Ke
• 0 • written 24 months ago by
kieran.short
▴ 40
4
votes
5
replies
1.9k
views
time course microarray data ArrayExpress database
R
GillespieColin
ArrayExpress
import
TimeSeriesExperiment
updated 6 months ago by
jacorvar
▴ 40 • written 18 months ago by
eraldagjika
▴ 20
4
votes
8
replies
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
Gordon Smyth
50k • written 16 months ago by
Sabiha
▴ 20
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 20 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
3
votes
4
replies
517
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats
r
RNASeqData
limma
voom
5 months ago
pl23
• 0
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 10 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 10 weeks ago by
Gordon Smyth
50k • written 4.7 years ago by
sambunga094
• 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
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 4 months ago by
Rory Stark
★ 5.1k • written 6.6 years ago by
kyliecode
• 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
1
vote
12
replies
2.4k
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
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
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
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
tanya
• 0
0
votes
3
replies
470
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
daenerystargaryen56
• 0 • written 4 months ago by
Sitapriya
• 0
0
votes
1
reply
621
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 11 months ago by
Gordon Smyth
50k • written 12 months ago by
qiz218591
• 0
0
votes
10
replies
791
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
505
views
Gene enrichment analysis
analysis
R
GOfuncR
updated 10 months ago by
Lluís Revilla Sancho
▴ 730 • written 10 months ago by
Eliza
• 0
0
votes
0
replies
108
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
7 weeks ago
danalvoronov
▴ 10
0
votes
2
replies
1.2k
views
Trouble Loading Data into Champ
loaddata
ChAMPdata
champload
R
ChAMP
updated 11 months ago by
hfbarrerat
• 0 • written 3.2 years ago by
Bethan
• 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
Rob
• 0 • written 5.5 years ago by
owen.donohoe
• 0
0
votes
2
replies
2.0k
views
Creating a qPCRset object from a text file
qPCRset object
nondetects
r
package
txt
updated 6 months ago by
Nat.Nataren
• 0 • written 6.3 years ago by
s.m.may
• 0
0
votes
6
replies
8.7k
views
No gene can be mapped error with clusterprofiler
clusterprofiler
r
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 7.3 years ago by
prp291
• 0
0
votes
4
replies
338
views
limma with interaction term
R
biostatistics
limma
Epigenetics
10 weeks ago • updated 8 weeks ago
Jitendra
▴ 10
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
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 5 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
0
votes
0
replies
215
views
multipollutant models
statistics
Regression
r
limma
4 months ago
Jitendra
▴ 10
0
votes
1
reply
489
views
DEseq2 Single cell data paired design
R
updated 12 months ago by
Marek Gierlinski
▴ 30 • written 12 months ago by
Caro
• 0
32 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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