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TCGAbiolinks
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
6 weeks ago • updated 4 weeks ago
Giovanni Calice
▴ 160
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 4 weeks ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
0
votes
1
reply
205
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 5 weeks ago by
BioinfoMug
• 0
1
vote
0
replies
142
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
7 weeks ago
BioinfoMug
• 0
0
votes
4
replies
960
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 8 weeks ago by
Marcel Ramos
690 • written 23 months ago by
Emre
• 0
0
votes
0
replies
137
views
GDC slides download
TCGAbiolinks
8 weeks ago
jain72744
• 0
0
votes
4
replies
255
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 9 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 9 weeks ago by
tirordep
• 0
0
votes
0
replies
138
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
10 weeks ago
Thalita
• 0
0
votes
1
reply
367
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
5 months ago
leon
• 0
0
votes
1
reply
599
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 8 months ago by
wrab425
• 0 • written 13 months ago by
snijesh
▴ 20
0
votes
0
replies
238
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
9 months ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
1.1k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago • updated 10 months ago
Habil Zare
▴ 200
0
votes
2
replies
832
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
12 months ago • updated 11 months ago
qiz218591
• 0
13 results • Page
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Comment: DESeq2 setting significant p-value
by
Michael Love
41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Votes
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
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