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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
5 hours ago
rocanja
▴ 60
1
vote
3
replies
2.8k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 7 hours ago by
snijesh
▴ 20 • written 6.4 years ago by
Ramiro Magno
▴ 100
0
votes
0
replies
14
views
Error in msaFun Cannot open input file. No alignment!
msa
12 hours ago
Kamil Slowikowski
▴ 30
1
vote
3
replies
97
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 8 hours ago by
Gordon Smyth
50k • written 23 hours ago by
JKim
• 0
0
votes
0
replies
22
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
14 hours ago
Julie
• 0
0
votes
0
replies
19
views
Help with Complex DESeq2 Design
DESeq2
14 hours ago
kelsey.beavers
• 0
4
votes
2
replies
70
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
21 hours ago • updated 11 hours ago
Georg
• 0
1
vote
0
replies
40
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
20 hours ago
andrebolerbarros
▴ 30
3
votes
15
replies
2.5k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
8 months ago • updated 23 hours ago
shepherl
3.8k
2
votes
2
replies
109
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
1 day ago • updated 20 hours ago
Eva
▴ 10
0
votes
3
replies
90
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
updated 59 minutes ago by
James W. MacDonald
65k • written 1 day ago by
Efra
• 0
3
votes
4
replies
112
views
DEG Filtering
MicroarrayData
limma
Genefiltering
2 days ago • updated 20 minutes ago
Amit
• 0
0
votes
1
reply
204
views
News:
BioC2024 abstract submission is open!
BioC2024
Conference
Bioconductor
updated 6 hours ago by
howell
• 0 • written 28 days ago by
Maria Doyle
▴ 70
0
votes
0
replies
86
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
14 days ago • updated 4 hours ago
Giovanni Calice
▴ 160
1
vote
2
replies
585
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 8 months ago by
malat1_t
▴ 10
0
votes
2
replies
1.0k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 2 hours ago by
william
• 0 • written 17 months ago by
Maria Doyle
▴ 70
0
votes
3
replies
1.2k
views
Error in ImportRData
dplyr
IsoformSwitchAnalyzeR
written 11 months ago by
ramon.dslps
• 0
2
votes
5
replies
1.2k
views
Downloading count matrix for full recount3 dataset
recount3
updated 23 hours ago by
Leonardo Collado Torres
★ 1.0k • written 2.7 years ago by
Ben
• 0
0
votes
1
reply
1.0k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST
AIC calcuation
Parameters
single cell
hurdle model
updated 17 hours ago by
rproendo
▴ 20 • written 5.1 years ago by
mcalgaro93
• 0
19 results • Page
1 of 1
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Comment: DEG Filtering
by
Amit
• 0
Hello Gordon, The PCA plot for RMA normalized data shows Mixing of samples. Is it Batch Effect ? Because when I apply ARSyNseq() and again …
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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