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gdcprepare
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1.3k
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Error in GDCDownload and GDCPrepare for TCGA-PAAD Dataset
GDCPrepare
GDCDownload
2.7 years ago
Manav
• 0
0
votes
0
replies
1.8k
views
GDCprepare error in TCGAbiolinks
tcgabiolinks
gdcprepare
differential expression
5.5 years ago
fawazfebin
▴ 60
4
votes
5
replies
3.2k
views
GDCprepare - error
TCGABiolinks
GDCprepare
5.8 years ago
vm
▴ 30
2
votes
2
replies
1.9k
views
TCGAbiolinks GDCprepare error
TCGAbiolinks
GDCprepare
error
updated 5.8 years ago by
Tiago C. Silva
▴ 270 • written 5.8 years ago by
Talip
▴ 10
1
vote
5
replies
2.1k
views
Issue with TCGAbiolinks package.
TCGA
GDCprepare
6.2 years ago
salvocomplicazioni1
• 0
0
votes
2
replies
2.4k
views
GDCprepare stop working for some unknown reason
tcgabiolinks
gdcprepare
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
ansari.sarabio
• 0
0
votes
0
replies
1.1k
views
Reasoning for illegal operation
tcgabiolinks
illegaloperation
gdcprepare
7.4 years ago
lisa8191
• 0
0
votes
1
reply
2.0k
views
How to get treatment information with TCGAbiolinks?
gdcprepare
tcgabiolinks
treatment_type
R
data extraction
updated 7.8 years ago by
Dario Strbenac
★ 1.6k • written 7.9 years ago by
newbie
• 0
0
votes
3
replies
1.6k
views
TCGA controlled data
R
tcgabiolinks
gdcprepare
7.9 years ago
ugandhar.ch1
• 0
0
votes
2
replies
4.2k
views
Extract gene expression values from GDCprepare object
tcgabiolinks
tcga
tcgadownload
gdcprepare
gdc
updated 8.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 8.2 years ago by
enigmargs
• 0
0
votes
8
replies
3.2k
views
TCGAbiolinks GDCprepare fails to connect to Biomart web server
tcgabiolinks
gdcprepare
8.6 years ago
sabarinath.chandrasekharan
▴ 10
0
votes
1
reply
1.4k
views
Error during GDCprepare
tcgabiolinks
gdcprepare
updated 8.7 years ago by
Tiago C. Silva
▴ 270 • written 8.7 years ago by
Mariana Boroni
▴ 10
12 results • Page
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Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
donnycrimson
• 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
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remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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