User: pv

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pv0
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Posts by pv

<prev • 9 results • page 1 of 1 • next >
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Comment: C: PCA plot after batch normalization
... Thank you for help. Can you suggest how to add colour to PCA plot? I tried the following: autoplot(prcomp(t(norm1),scale. = TRUE, colour="control")) and other one: autoplot(prcomp(t(norm1),scale. = TRUE, colby="control")) but it is giving error: Warning message: In prcomp.default(t(no ...
written 7 days ago by pv0
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PCA plot after batch normalization
... I have two microarray datasets with same platform. I performed batch normalization using: norm1=removeBatchEffect(norm, batch=NULL, batch2=NULL, covariates=NULL, design=matrix(1,ncol(norm),1)) and now I want a PCA plot of test and control samples. I tried using the following codes: #pca ...
R written 9 days ago by pv0 • updated 9 days ago by Kevin Blighe54k
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Comment: C: how to get gene symbol from Entrez id
... - thank you for your suggestion. - But after adding this filter, the sequence of the IDs changed. I want them in the original sequence (list). Can you suggest how to do it? -And also the number of IDs decreased compared to the original list. What can be the reason for that? ...
written 12 days ago by pv0
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Comment: C: how to get gene symbol from Entrez id
... Thank you, I used given code with small changes: gene<-getBM(attributes = c("entrezgene_id","external_gene_name"), values = rownames(Ra_mod), mart=mart) and i got results: entrezgene_id external_gene_name 1 NA MT-TF 2 NA MT-RNR1 3 ...
written 13 days ago by pv0
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Comment: C: how to get gene symbol from Entrez id
... I have a long list of genes, so individual ID will take time. And I want Gene names or Gene symbols, not Ensembl IDs. ...
written 13 days ago by pv0
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Comment: C: how to get gene symbol from Entrez id
... yes, I read all these posts, but nothing seems to be working. ...
written 13 days ago by pv0
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Comment: C: summarized experiment in R
... As I have very basic knowledge about R. Can you suggest how can I modify them? ...
written 19 days ago by pv0
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Comment: A: summarized experiment in R
... I tried running this command : nrows <- 20962 ncols <- 93 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows) colData <- DataFrame(sample="1:20962", row.names= paste("sample", letters[5:1])) sumex <- SummarizedExperiment(assays=SimpleList(counts=counts), ...
written 19 days ago by pv0 • updated 19 days ago by zx87549.0k
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summarized experiment in R
... I am learning R language and trying some basic analysis with datasets. I normalized the data and converted it to gene level from probe level. But now, while working with summarized experiment package, I am facing lots of error. So, anyone can please suggest correct workflow and R script for summariz ...
R written 19 days ago by pv0 • updated 19 days ago by Asaf7.0k

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