User: helen

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helen20
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Posts by helen

<prev • 12 results • page 1 of 2 • next >
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Comment: C: How to interpret DESeq2 result?
... 1. Yes, Sex would be more appropriate. Thanks for pointing it out. For 2. & 3. I think I misunderstood what the result is trying to tell. I thought this design is to compare condition A vs. B under specific sex, but in fact this interpretation is not correct. If I understand correctly, the fewer ...
written 6 days ago by helen20
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Answer: A: DESeq2 design formula with paired samples
... My updated post is here: https://www.biostars.org/p/447684/ ...
written 7 days ago by helen20
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How to interpret DESeq2 result?
... Hi all, I have 6 subjects 1-6, and would like to identify the differentially expressed genes in condition A vs.B and consider the gender effect. I arrange my coldata as follow to mimic the example in this section of DESeq2 manual: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/ ...
deseq2 rna-seq written 7 days ago by helen20
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DESeq2 design formula with paired samples
... I have 6 subjects 1-6, and would like to identify the differentially expressed genes in condition A vs.B and considering the gender effect. Here is my coldata: subject gender condition 1 m A 1 m B 2 m A 2 m ...
deseq2 rna-seq written 10 days ago by helen20
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Comment: C: How to solve DESeq2 Error in checkFullRank(modelMatrix)?
... Thank you, Asaf. It works! ...
written 13 days ago by helen20
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How to solve DESeq2 Error in checkFullRank(modelMatrix)?
... I have 4 factors in the design formula in DESeq2 dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition + gender + batch + genotype) but got an error Error in checkFullRank(modelMatrix) ...
deseq2 rna-seq written 14 days ago by helen20 • updated 14 days ago by Asaf8.1k
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What result from DESeq2 should be used as an input for volcano plot?
... My cutoff for differentially expressed genes (DEGs) is **adjusted *P* < 0.05** and **|log2FoldChange| > 1**. I used this code in DESeq2 to get those DEGs: library(DESeq2) cts <- as.matrix(read.csv("GE_counts_Sst.csv",row.names="gene")) coldata <- read.csv('coldata_Sst.csv', ...
enhancedvolcano deseq2 volcano plot rna-seq written 21 days ago by helen20 • updated 4 days ago by MaxF50
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How to deal with sample size problem in GWAS meta-analysis
... When conducting the meta-analysis of multiple GWAS summary data, my result was dominated by one GWAS data due to its large sample size (~10 fold to other GWAS data). Does anyone know how to deal with this problem to avoid bias? Thank you for any solution. ...
gwas meta-analysis written 4 weeks ago by helen20
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Comment: C: Specifying sample size from GWAS summary statistics for meta-analysis
... Thank you, Sam. Then what if I have another sumstat that doesn't have any information regarding the sample size. Would you recommend me to calculate the effective sample size from the raw sample size mentioned in the original paper and transform it using the statistic methods like in the linked arti ...
written 4 weeks ago by helen20
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Specifying sample size from GWAS summary statistics for meta-analysis
... The meta-analysis tool I am using (METAL) requires users to specify Weight (sample size) from each GWAS summary statistics file. I have a sumstat file contains columns Nca, Nco, and Neff, but the Neff does not equal to the value of Nca + Nco. I was wondering what the sample size means here? Should I ...
snp written 4 weeks ago by helen20 • updated 4 weeks ago by Sam3.0k

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