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tcgabiolinks
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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
0
votes
0
replies
132
views
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
0
replies
143
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
0
replies
138
views
GDC slides download
TCGAbiolinks
8 weeks ago
jain72744
• 0
0
votes
4
replies
257
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
139
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
11 weeks ago
Thalita
• 0
0
votes
1
reply
370
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
5 months ago
leon
• 0
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
834
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
12 months ago • updated 11 months ago
qiz218591
• 0
0
votes
1
reply
600
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
4
replies
960
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 8 weeks ago by
Marcel Ramos
690 • written 24 months ago by
Emre
• 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 4 weeks ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
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by
Gordon Smyth
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Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
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prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
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Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
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