Showing : TCGAbiolinks • reset
0
votes
0
replies
154
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
9 weeks ago • updated 7 weeks ago Giovanni Calice ▴ 160
1
vote
3
replies
3.1k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error maftools tcgabiolinks
updated 7 weeks ago by ▴ 20 • written 6.6 years ago by ▴ 100
0
votes
1
reply
235
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks TCGA clinical TCGA-BRCA
written 8 weeks ago by • 0
1
vote
0
replies
177
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
10 weeks ago BioinfoMug • 0
0
votes
4
replies
1.0k
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 10 weeks ago by 690 • written 2.0 years ago by • 0
0
votes
0
replies
171
views
GDC slides download
TCGAbiolinks
11 weeks ago jain72744 • 0
0
votes
4
replies
303
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 12 weeks ago by ▴ 730 • written 12 weeks ago by • 0
0
votes
0
replies
159
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks ChAMP
3 months ago Thalita • 0
0
votes
1
reply
411
views
Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
6 months ago leon • 0
0
votes
1
reply
625
views
How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 8 months ago by • 0 • written 14 months ago by ▴ 20
0
votes
0
replies
254
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical TCGAbiolinks
10 months ago BioInfoBeginnerrr • 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago Habil Zare ▴ 200
0
votes
2
replies
870
views
RPPA data (Proteomics analysis)
TCGAbiolinks limma
13 months ago • updated 12 months ago qiz218591 • 0
1
vote
1
reply
781
views
Error when running getGDCprojects()
TCGAbiolinks
14 months ago DevelopingHippo • 0
0
votes
0
replies
562
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival TCGAbiolinks R PAAD
14 months ago Manav • 0
1
vote
2
replies
1.6k
views
Error when running GDC_prepare
TCGAbiolinks
14 months ago DevelopingHippo • 0
1
vote
3
replies
949
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2 TCGAbiolinks
16 months ago Alexandre • 0
0
votes
0
replies
467
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
18 months ago lescano ▴ 10
0
votes
2
replies
2.1k
views
GDCprepare() - R Session Aborted
TCGAbiolinks R GDCprepare()
2.1 years ago • updated 19 months ago spyrouglykeria • 0
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years ago by • 0
0
votes
0
replies
646
views
Query on TCGA
TCGAbiolinks TCGAWorkflow
20 months ago hemangininaik09 • 0
0
votes
2
replies
1.4k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 21 months ago by ▴ 270 • written 22 months ago by • 0
2
votes
8
replies
4.9k
views
GDCquery_Maf error
TCGAbiolinks GDCquery_Maf
updated 21 months ago by • 0 • written 2.1 years ago by • 0
0
votes
0
replies
731
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks Proteomics GENOMICS bioinformatics
21 months ago qiz218591 • 0
0
votes
0
replies
529
views
TCGAbiolinks file.type argument
TCGAbiolinks
21 months ago Elizabeth • 0
0
votes
0
replies
547
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks TCGAbiolinksGUI.data SummarizedExperiment
23 months ago syednajeebashraf • 0
5
votes
4
replies
2.9k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 24 months ago by ★ 1.3k • written 2.1 years ago by ▴ 30
0
votes
2
replies
2.1k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks TARGET-AML
updated 2.0 years ago by ▴ 270 • written 2.1 years ago by • 0
2
votes
5
replies
1.6k
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
3
votes
2
replies
2.2k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC TCGA tcgabiolinks
updated 2.1 years ago by • 0 • written 5.5 years ago by ▴ 10
6
votes
3
replies
3.1k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.1 years ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
0
replies
575
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.1 years ago komal.rathi ▴ 120
0
votes
5
replies
1.5k
views
TCGAbiolinks installation error because of R.oo installation error
TCGAbiolinks R.oo
updated 2.3 years ago by • 0 • written 3.8 years ago by ▴ 10
0
votes
0
replies
814
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
2.4 years ago constantinosdem • 0
0
votes
0
replies
673
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq TCGAbiolinks TCGAAnalyze_DEA
2.5 years ago Gandino • 0
0
votes
1
reply
2.1k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
2.5 years ago raf4 ▴ 20
1
vote
2
replies
1.1k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
2.5 years ago raf4 ▴ 20
0
votes
1
reply
1.3k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks WGCNA
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
0
replies
727
views
DEGs for legacy and harmonized dataset
#DEGs #legacydataset #harmonizeddataset TCGAbiolinks
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
1
reply
1.2k
views
Help With TCGAbiolinks package
TCGAbiolinks data normalize l
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
0
votes
2
replies
1.1k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
2.9 years ago H. Z. Amini ▴ 10
0
votes
0
replies
1.6k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks TCGAWorkflowData
2.9 years ago H. Z. Amini ▴ 10
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
0
votes
0
replies
735
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA TCGAbiolinks
3.0 years ago rebeliscu • 0
0
votes
3
replies
940
views
discrepancy in number of samples
TCGAquery_recount2 TCGAbiolinks
3.1 years ago xiaofeiwang18266 ▴ 50
1
vote
1
reply
1.4k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks RECOUNT2 DESeq2
updated 3.1 years ago by 42k • written 3.1 years ago by ▴ 50
3
votes
8
replies
3.5k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.1 years ago xiaofeiwang18266 ▴ 50
0
votes
1
reply
769
views
error reading from connection
TCGAbiolinks
updated 3.1 years ago by ★ 3.9k • written 4.6 years ago by • 0
0
votes
0
replies
852
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
votes
1
reply
1.7k
views
TCGAbiolinks connection error for GDCquery
MethylationArray TCGAbiolinks
3.3 years ago Sophie Marion de Proce • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Awards • All
Popular Question to Gyan Prakash Mishra ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Locations • All
Australia, 2 minutes ago
United States, 16 minutes ago
India, 19 minutes ago
WEHI, Melbourne, Australia, 20 minutes ago
United States, 44 minutes ago
Traffic: 570 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6