User: evelyn
evelyn • 100
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Posts by evelyn
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... Thank you, I can see results. I have a question: do I need to do it for each gene separately or I can plug a list of genes to get GO terms for each gene. ...
written 2 days ago by
evelyn • 100
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... Thank you, I uploaded a plain text file with gene list. I selected reference list as available in the database. I chose GO biological process complete. It gave result and shows 250 genes are not mapped. But the number of genes from each category does not represent the actual total of genes in the li ...
written 3 days ago by
evelyn • 100
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... Thank you, I have list of 1500 genes. These came from a different genome for the same species whose reference genome is included in PANTHER. So I changed the gene id's based on reference genome available. I uploaded the gene list here http://www.pantherdb.org and chose file type (ID list), organism ...
written 3 days ago by
evelyn • 100
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... Thank you! I have a list of genes that I want to find gene ontology terms for. I looked at pantherdb, can I plug a list of genes and get results for all together or do I need to plug one gene at a time, ...
written 3 days ago by
evelyn • 100
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... Hi,
I have multiple sample RNA-seq data. I have the gene annotations gff file. I want to find gene ontology terms for the genes. Can you please suggest a way.
Thank you! ...
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... Hello,
I have a vcf file with 200 samples. I need only 100 specific samples out of the 200 in total for some downstream analysis. I there a way to filter out these samples without parsing vcf or changing the file format.
Thank you! ...
written 4 days ago by
evelyn • 100
• updated
4 days ago by
WouterDeCoster ♦ 44k
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... Hello,
I have an expression data matrix and phenotype data. I started with SNPRelate to get the PCA and IBS analysis using:
library(SNPRelate)
library(gdsfmt)
#Convert vcf file to gds file
vcf.fn <- "data.vcf"
snpgdsVCF2GDS(vcf.fn, "test.gds", method="biallelic.only")
...
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Comment:
C: WGCNA heatmap error
... Thank you! Yes, I had 80 modules and I increased the values in 'greenWhiteRed()'. But still got the same error. ...
written 12 days ago by
evelyn • 100
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Comment:
C: WGCNA heatmap error
... Thank you, I have got `[1] TRUE TRUE` after checking the dimensions. ...
written 13 days ago by
evelyn • 100
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... Hello,
I am doing network analysis for RNA-seq using WGCNA. I have created the modules and now constructing phenotype module relationship. I am getting an error in the heat map step:
labeledHeatmap(Matrix = moduleTraitCor,
xLabels = colnames(datTraits),
yLabels ...
written 13 days ago by
evelyn • 100
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