User: Cece

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Cece0
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Posts by Cece

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Comment: C: Remove HB genes and recalculate read depth
... Oh, so simple. Now I feel somewhat simple! Thanks so much for clearing this up for me :) ...
written 11 months ago by Cece0
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Comment: C: Remove HB genes and recalculate read depth
... Hi Devon, Thanks for the response but I still don't understand. I've removed the HB genes from my counts matrix but still have no idea how I go about checking what the read depth of my matrix is. ...
written 11 months ago by Cece0
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Comment: C: Remove HB genes and recalculate read depth
... For summarization, I want to check if my mean read depth is still a minimum of 30 million. I'm not sure how to do that from the counts matrix. Previously, I used the fastqc/ multiqc summaries to check read depth. ...
written 11 months ago by Cece0
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Comment: C: Remove HB genes and recalculate read depth
... Yes, my counts are raw counts. Excuse me if I'm using the wrong language; I guess what I'm asking is if there is a way to summarize read depth for my counts in R after removing the HB genes. Alternatively, is the best way to do this to somehow remove the HB genes during mapping so that when I summar ...
written 11 months ago by Cece0
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Remove HB genes and recalculate read depth
... Hi All, I have a counts matrix from rsubread/ featureCounts which I've used in DESeq2 for differential gene expression. I've noticed that the HB genes are skewing my analysis so I'd like to remove them. From reading around, it appears that I can extract these from the counts matrix before normaliza ...
rnaseq read depth hemoglobin written 11 months ago by Cece0
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Comment: C: DESeq2: subset dds or vsd to plot PCA with specific genes only
... Thanks, Kevin, Subsetting vsd worked great for me. I've also looked at PCATools, which looks really comprehensive but a little intimidating to me. My counts data is in a text file, with genes as rows and columns as samples: sample1 sample2 sample3 gene1 1063 1092 ...
written 14 months ago by Cece0
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DESeq2: subset dds or vsd to plot PCA with specific genes only
... Hi All, I've run DESeq2 on my counts comparing two conditions, treated vs untreated. I have my dds object and have generated my vsd object using the command: vsd <- vst(dds, blind = FALSE) then plotted my PCA using: plotPCA(vsd, intgroup = "condition", ntop = 500) However, I'd like t ...
R deseq2 plotpca rna-seq subset written 14 months ago by Cece0 • updated 14 months ago by Kevin Blighe59k
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edgeR DE; choosing right coefficient from design matrix with many covariates
... Hi, I'm trying to run a DE analysis in edgeR and I'm getting confused trying to choose the right coefficient from the model matrix. Group is a factor made up of cases and controls (disease analysis), Gender is a factor (Male and Female), and Age and Cov1 are continuous. My design looks like: desig ...
rna-seq edger written 20 months ago by Cece0
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Allele Frequency correlation in R
... Hi,   I'm trying to run a correlation of allele frequencies of my two populations. My datasets are from plink so I imported them into R with read.plink. Problem is, R says they're matrices. I was trying to use cor.test but data has to be numeric. I tried to transform them to numeric using as.data. ...
myposts written 4.3 years ago by Cece0
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Comment: C: Count numbers of population level and sample level SNPs in my vcf
... Thanks, but I'm learning python as well as bioinformatics so I'm working on learning how to write my own scripts. ...
written 4.9 years ago by Cece0

Latest awards to Cece

Popular Question 19 months ago, created a question with more than 1,000 views. For Allele Frequency correlation in R
Popular Question 21 months ago, created a question with more than 1,000 views. For Allele Frequency correlation in R
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Help Parsing vcf for indels and splice sites

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