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picksoftthreshold
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Drop of soft-threshold curve with high power values
wgcna
picksoftthreshold
scale-free topology
co-expression network
5.9 years ago
marcantoine.guery
• 0
2
votes
0
replies
1.9k
views
'Error in summary(lm1)$coefficients[2, 1] : subscript out of bounds' while running pickSoftThreshold in WGCNA
wgcna
picksoftthreshold
6.0 years ago
aditi
▴ 20
1
vote
1
reply
1.7k
views
WGCNA - Choosing the best threshold
wgcna
sft
picksoftthreshold
threshold
rnaseq
updated 6.1 years ago by
Peter Langfelder
★ 2.9k • written 6.1 years ago by
Fabricio Almeida-Silva
▴ 40
0
votes
3
replies
1.7k
views
Unable to get soft threshold power using WGCNA for RNA-seq data
rnaseq
wgcna
picksoftthreshold
updated 7.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.4 years ago by
divara01
• 0
0
votes
2
replies
4.0k
views
WGCNA - problems picking a suitable power
WGCNA
pickSoftThreshold
power
RNA-Seq
updated 8.1 years ago by
Peter Langfelder
★ 2.9k • written 8.1 years ago by
mrodrigues.fernanda
▴ 10
5 results • Page
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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…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
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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