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GDCprepare
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0
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716
views
Error in GDCDownload and GDCPrepare for TCGA-PAAD Dataset
GDCPrepare
GDCDownload
20 months ago
Manav
• 0
0
votes
0
replies
1.4k
views
GDCprepare error in TCGAbiolinks
tcgabiolinks
gdcprepare
differential expression
4.5 years ago
fawazfebin
▴ 60
4
votes
5
replies
2.5k
views
GDCprepare - error
TCGABiolinks
GDCprepare
4.8 years ago
vm
▴ 30
2
votes
2
replies
1.5k
views
TCGAbiolinks GDCprepare error
TCGAbiolinks
GDCprepare
error
updated 4.8 years ago by
Tiago C. Silva
▴ 270 • written 4.8 years ago by
Talip Zengin
▴ 10
1
vote
5
replies
1.6k
views
Issue with TCGAbiolinks package.
TCGA
GDCprepare
5.2 years ago
salvocomplicazioni1
• 0
0
votes
2
replies
1.8k
views
GDCprepare stop working for some unknown reason
tcgabiolinks
gdcprepare
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
ansari.sarabio
• 0
0
votes
0
replies
832
views
Reasoning for illegal operation
tcgabiolinks
illegaloperation
gdcprepare
6.4 years ago
lisa8191
• 0
0
votes
1
reply
1.6k
views
How to get treatment information with TCGAbiolinks?
gdcprepare
tcgabiolinks
treatment_type
R
data extraction
updated 6.9 years ago by
Dario Strbenac
★ 1.5k • written 6.9 years ago by
newbie
• 0
0
votes
3
replies
1.4k
views
TCGA controlled data
R
tcgabiolinks
gdcprepare
6.9 years ago
ugandhar.ch1
• 0
0
votes
2
replies
3.7k
views
Extract gene expression values from GDCprepare object
tcgabiolinks
tcga
tcgadownload
gdcprepare
gdc
updated 7.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 7.2 years ago by
enigmargs
• 0
0
votes
8
replies
2.6k
views
TCGAbiolinks GDCprepare fails to connect to Biomart web server
tcgabiolinks
gdcprepare
7.6 years ago
sabarinath.chandrasekharan
▴ 10
0
votes
1
reply
1.2k
views
Error during GDCprepare
tcgabiolinks
gdcprepare
updated 7.7 years ago by
Tiago C. Silva
▴ 270 • written 7.7 years ago by
Mariana Boroni
▴ 10
12 results • Page
1 of 1
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Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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