User: candida.vaz

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candida.vaz30
Reputation:
30
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New User
Location:
Singapore
Last seen:
2 years, 6 months ago
Joined:
3 years ago
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c**********@gmail.com

Posts by candida.vaz

<prev • 14 results • page 1 of 2 • next >
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Answer: A: What are logCPM values in the Differentially Expressed Genes output
... Dear Sir, Thank you very much for the help. It is clear to me now. Regards, Candida ...
written 2.5 years ago by candida.vaz30
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What are logCPM values in the Differentially Expressed Genes output
... Dear edgeR support team,  I am not clear about the logCPM values in the Differentially Expressed genes output (logCPM column along with the columns of logFC and p-values and FDR) What do they represent?   Thanks a lot, Candida Vaz ...
edger written 2.5 years ago by candida.vaz30
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Batch effect removal in edgeR
... Dear edgeR support team, In the tutorial its mentioned that Batch effects can be removed or corrected by using the additive model formula. How can I visualise the removal of batch effect on the clustering of the samples using edgeR. Thanks and Regards, Candida ...
edger batch effect written 2.8 years ago by candida.vaz30 • updated 2.8 years ago by Gordon Smyth32k
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Answer: A: Doubt about the "zero expression" genes or genes with no reads at all in the co
... Dear James and Gordon, Thank you very much for clearing my doubt. I know that the observed fold change is actually infinite in this case. And yes, it is representative of the underlying biology. I just wanted to make sure I wasn't missing out on any step in edgeR and have followed all the steps cor ...
written 2.9 years ago by candida.vaz30
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Doubt about the "zero expression" genes or genes with no reads at all in the count matrix file
... As it is mentioned in the edgeR tutorial that the count matrix or table of read counts should be actual values representing total number of reads mapping to a gene. There are some genes with no reads mapping at all, hence have zero values for some samples, whereas for some samples they have very hig ...
edger written 2.9 years ago by candida.vaz30
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Comment: C: TreatDGE function usage
... Thanks Aaron, Yes I have removed the corresponding column in the count matrix. Thanks for the help! Candida ...
written 2.9 years ago by candida.vaz30
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Answer: A: TreatDGE function usage
... Dear Gordon, Thanks a lot for your prompt reply, I read in the edge R tutorial that "0+ in the model formula is an instruction not to include an intercept column and instead to include a column for each group". so I decided to fit my design matrix as: "design <- model.matrix(~0+group)" x < ...
written 2.9 years ago by candida.vaz30
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TreatDGE function usage
... Dear EDGER support team, I have a single factor experiment with the 5 different samples having three replicates each. group <- factor(c("a","a","a","b","b","b","c","c","c","d","d","d","e","e","e")) Using a GLM based approach, and using TreatDGE function, I am trying to obtain the Differentiall ...
edger written 2.9 years ago by candida.vaz30
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Comment: C: Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
... Thank you very much Aaron. I guess all my doubts are cleared now! Just one last check:- So once I run the first contrast (2 vs 1) and get the DE list as follows:  fit <- glmFit(y, design) tr <- treatDGE(fit, coef=2, lfc=1) out <- topTags(tr, n=Inf, adjust.method="BH") keep <- out$tabl ...
written 2.9 years ago by candida.vaz30
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Comment: C: Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
... Thanks a lot Aaron, Just a last bit of clarification:- 1. To get the TMM normalised values in a file. Are the following lines ok? y <- calcNormFactors(y) norm.vals <- cpm(y) write.table(norm.vals, file="TMM_edgeR_Normalized.txt", row.names = TRUE, col.names = NA, quote=FALSE, sep = "\t")--- ...
written 2.9 years ago by candida.vaz30

Latest awards to candida.vaz

Great Question 2.5 years ago, created a question with more than 5,000 views. For Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Batch effect removal in edgeR
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off

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