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Showing :
batch-effect
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0
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711
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Export Results from BatchQC Shiny App
BatchQC
RNA-seq
R
Shiny
batch-effect
3.9 years ago
manninm
• 0
4
votes
4
replies
2.2k
views
Average read counts and batch-effect correction in edgeR
edgeR
batch-effect
RNA-seq
read counts
ngs
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Roman
▴ 20
3
votes
7
replies
2.0k
views
Batch effects between controls
batch-effect
ruvseq
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
llo
▴ 10
2
votes
5
replies
5.6k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
rmf
▴ 20
4 results • Page
1 of 1
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Replies
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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James W. MacDonald
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Gordon Smyth
50k
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rocanja
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Wolfgang RAFFELSBERGER
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