Showing : TCGABiolinks • reset
2
votes
11
replies
3.7k
views
package or namespace load failed for TCGAbiolinks
tcgabiolinks
updated 6.5 years ago by ▴ 200 • written 6.6 years ago by • 0
1
vote
3
replies
3.0k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ▴ 100
2
votes
22
replies
4.2k
views
Error in 'colnames' while running case 1 of TCGABiolinks
tcgabiolinks Error in `colnames
8.2 years ago zeeniajagga • 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
1
vote
2
replies
1.5k
views
TCGABiolinks::GDCquery() suddenly sending back unknown error
software error error tcgabiolinks GDCquery
updated 6.5 years ago by ▴ 40 • written 6.5 years ago by ▴ 10
6
votes
11
replies
3.0k
views
Error and weird result of TCGAanalyze_Normalization function using the R package TCGAbiolinks for normalization of raw HTSeq counts
tcgabiolinks rnaseq normalization EDASeq
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 830
6
votes
7
replies
2.5k
views
Differences between RTCGA and TCGAbiolinks data
r survival analysis rtcga tcgabiolinks mirna-seq
5.9 years ago atakanekiz ▴ 30
6
votes
3
replies
2.2k
views
TCGAbiolinks GDCquery Error: Parsing problems
tcgabiolinks
updated 6.5 years ago by ▴ 50 • written 6.5 years ago by ▴ 100
0
votes
5
replies
2.7k
views
Retrieve TCGA expression data for a single gene
TCGA TCGAbiolinks
updated 3.6 years ago by ▴ 260 • written 3.6 years ago by ▴ 40
0
votes
6
replies
3.0k
views
TCGAbiolinks DNA methylation analysis TCGAvisualize_meanMethylation
tcgabiolinks
updated 8.1 years ago by ▴ 270 • written 8.1 years ago by ▴ 10
1
vote
7
replies
2.0k
views
Cannot retrieve projects from TCGA using getGDCprojects function
tcgabiolinks TCGA software error
6.4 years ago jacorvar ▴ 40
0
votes
11
replies
3.2k
views
TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
tcgabiolinks gdc
7.5 years ago • updated 7.4 years ago jshelton • 0
4
votes
2
replies
2.2k
views
TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
tcgabiolinks grch38 annotation
updated 6.5 years ago by ▴ 270 • written 6.6 years ago by • 0
1
vote
3
replies
2.5k
views
Data download via TCGAbiolinks
tcgabiolinks
updated 6.9 years ago by • 0 • written 8.3 years ago by ▴ 10
3
votes
2
replies
2.1k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.0 years ago by • 0 • written 5.4 years ago by ▴ 10
7
votes
6
replies
2.4k
views
Analysis using TCGAbiolinks
tcgabiolinks triple negative breast cancer data sets
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 60
5
votes
4
replies
2.8k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 23 months ago by ★ 1.3k • written 2.1 years ago by ▴ 30
0
votes
4
replies
2.2k
views
TCGA biolinks data download
tcgabiolinks
updated 7.8 years ago by ▴ 270 • written 7.8 years ago by ▴ 10
2
votes
5
replies
1.5k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks TCGA
updated 2.0 years ago by • 0 • written 3.6 years ago by ▴ 40
0
votes
2
replies
2.6k
views
Unable to install TCGAbiolinks
tcgabiolinks
updated 6.6 years ago by 3.8k • written 6.6 years ago by • 0
2
votes
5
replies
3.6k
views
GDCdownload does not work
GDCdow tcgabiolinks error tcgadownload download_error
updated 5.4 years ago by ▴ 260 • written 5.4 years ago by • 0
1
vote
2
replies
1.4k
views
Problem with TCGAbiolinks Enrichment analysis
tcgabiolinks
updated 6.8 years ago by • 0 • written 6.9 years ago by ▴ 10
4
votes
20
replies
3.1k
views
TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid for atomic vectors
tcgabiolinks
updated 7.0 years ago by ★ 6.5k • written 7.0 years ago by ▴ 190
5
votes
11
replies
3.9k
views
Matching TCGA Aliquot ID to UUID or Barcode
TCGAutils TCGAbiolinks GenomicDataCommons
updated 4.8 years ago by 690 • written 4.8 years ago by ★ 1.5k
1
vote
2
replies
1.1k
views
Downloading bt.exon_quantification with TCGAbiolinks
tcgabiolinks bug
8.0 years ago Marcel Ramos 690
0
votes
1
reply
1.2k
views
Error during GDCprepare
tcgabiolinks gdcprepare
updated 7.6 years ago by ▴ 270 • written 7.7 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Missing the package called 'R.oo'. Please help me to fix, thanks.
TCGAbiolinks
updated 8.0 years ago by ▴ 150 • written 8.0 years ago by • 0
1
vote
6
replies
2.0k
views
Errors in TCGAbiolinks
tcgabiolinks
updated 7.7 years ago by ▴ 260 • written 7.7 years ago by ▴ 10
0
votes
7
replies
1.8k
views
TCGAbiolinks not downloading the 450k data
tcgabiolinks
updated 7.6 years ago by ▴ 260 • written 7.6 years ago by ▴ 190
0
votes
3
replies
4.3k
views
Problem in downloading data via TCGAbiolinks
tcgabiolinks tcgadownload
updated 2.9 years ago by ▴ 10 • written 7.8 years ago by ▴ 10
1
vote
3
replies
5.7k
views
package ‘TCGAbiolinks’ is not available (for R version 3.2.0)
software error TCGAbiolinks
updated 8.3 years ago by 25k • written 8.3 years ago by • 0
0
votes
2
replies
1.3k
views
Problems running TCGAbiolinks
tcgabiolinks
updated 7.8 years ago by ▴ 270 • written 7.8 years ago by • 0
0
votes
3
replies
1.4k
views
TCGA controlled data
R tcgabiolinks gdcprepare
6.9 years ago ugandhar.ch1 • 0
1
vote
5
replies
1.2k
views
update TCGAbiolinks to version 3.6 and GDCquery doesn't work
software error tcgabiolinks
updated 6.5 years ago by ▴ 40 • written 6.5 years ago by • 0
1
vote
2
replies
1.5k
views
TCGAbiolinks download and read data error
TCGAbiolinks
updated 7.8 years ago by ▴ 270 • written 7.8 years ago by • 0
1
vote
1
reply
1.4k
views
TCGAbiolinks download error
tcgabiolinks TCGAdownload
updated 7.8 years ago by ▴ 270 • written 7.8 years ago by ▴ 20
0
votes
3
replies
1.3k
views
TCGAbiolinks Genome_Wide_SNP_6 data analysis
tcgabiolinks
updated 8.1 years ago by ▴ 260 • written 8.1 years ago by ▴ 10
0
votes
1
reply
779
views
Meaning of subtype_methylation.Clusters , subtype_miRNA.Clusters, subtype_CN.Clusters
tcgabiolinks
updated 7.2 years ago by ▴ 260 • written 7.2 years ago by • 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 ▴ 260 • written 7.2 years ago by • 0
1
vote
2
replies
1.5k
views
TCGAbiolinks 403 Forbidden Error
bug issue tcgabiolinks
updated 7.8 years ago by ▴ 270 • written 7.9 years ago by 690
0
votes
1
reply
1.1k
views
Error downloading the package
tcgabiolinks TCGA DOWNLOAD
updated 6.6 years ago by 65k • written 6.6 years ago by ▴ 30
0
votes
1
reply
1.2k
views
maybe problem with TCGAdownload function
TCGAbiolinks
7.9 years ago hibari.kyouya • 0
1
vote
3
replies
1.3k
views
TCGAbiolinks FTP address
tcgabiolinks
updated 8.2 years ago by ★ 6.5k • written 8.2 years ago by ▴ 10
1
vote
1
reply
948
views
Problem with using GDC_queryMaf()
tcgabiolinks maf mutations
updated 7.1 years ago by ▴ 260 • written 7.2 years ago by ▴ 150
1
vote
2
replies
1.5k
views
Multiple problems with TCGAbiolinks 2.2.6
software error tcgabiolinks ubuntu
updated 7.4 years ago by ▴ 260 • written 7.4 years ago by • 0
0
votes
2
replies
3.5k
views
Error using TCGAbiolinks "Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column"
TCGA tcgabiolinks Error
6.9 years ago f.geist ▴ 20
0
votes
1
reply
805
views
Data type error
tcgabiolinks
updated 7.4 years ago by ▴ 260 • written 7.4 years ago by • 0
1
vote
1
reply
1.9k
views
Install problems on centos 7 of TCGAbiolinks
tcgabiolinks centos7
updated 7.4 years ago by ★ 6.5k • written 7.4 years ago by ▴ 40
2
votes
6
replies
2.0k
views
Using TCGAbiolinks for exon and oligonucleotide level microarray
tcga tcgabiolinks microarray exons oligonucleotide
updated 7.9 years ago by ▴ 270 • written 8.0 years ago by • 0
1
vote
1
reply
793
views
TCGAbiolinks XML error
tcgabiolinks
updated 6.6 years ago by • 0 • written 6.8 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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