## User: myprogramming2016

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3 years, 8 months ago
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#### Posts by myprogramming2016

<prev • 34 results • page 2 of 4 • next >
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... Hi Aaron, I estimated homologous gene and GO annotation for each of the transcript using Arabidopsis genome. I am not clear with defining all transcripts belonging to a single GO term as a gene set. Could you please send me an example file and R code for roast and camera? Thanks for your help!   ...
written 3.4 years ago by myprogramming20160
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... Hi,  I am working on plant dataset which is a close relative of Arabidopsis.  I performed differential expression analysis using an edgeR and found significant DE genes. I would like to identify associated GO terms.  I have a transcript as a Scaffold, and not the ENTREZ ID.  I am just wondering w ...
written 3.4 years ago by myprogramming20160
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... Thanks Ryan for the explanation. ...
written 3.5 years ago by myprogramming20160
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... Hi, I have a question about interpreting contrast. I have three conditions, for e.g. high, med and low. I am interesting in looking at the genes which are differentially expressed in high condition over others. I am using following code to look at High vs Low HvsL<-makeContrasts(high - low,le ...
written 3.5 years ago by myprogramming20160 • updated 3.5 years ago by Ryan C. Thompson7.4k
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Comment: C: design matrix in GLM
... Thanks for your help. ...
written 3.5 years ago by myprogramming20160
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Comment: C: design matrix in GLM
... Thanks for your comments on the code. You mean I should use glmQLFit() instead of glmFit + glmLRT. I am not quite sure. Please guide me   fit <- glmQLFit(y, design, robust=TRUE)  qlf <- glmQLFTest(fit)  topTags(qlf) In addition, I would like to subset DE data using 5% FDR and log-fold ...
written 3.5 years ago by myprogramming20160
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Comment: C: design matrix in GLM
... Thanks Aaron. I checked both the designs. They are yielding similar output.  Secondly, I have seen in the example case studies in the edgeR manual that they have used glmQFit().  I am just wondering whether I should use glmFit() or glmQFit()?  How do I decide? I have data in three biological repl ...
written 3.5 years ago by myprogramming20160
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... Hi, I am looking for differentially expressed genes between three different groups.  What is the preferred method of design matrix in GLM from the following?  design<-model.matrix(~0+group,data=y$samples) or design<-model.matrix(~group,data=y$samples) Thanks       ...
written 3.5 years ago by myprogramming20160 • updated 3.5 years ago by Aaron Lun25k
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Comment: C: Normalization in edgeR
... Thanks for your help. I have re-written the codes.  I would like to subset the read counts without converting them into CPM. I mean, subsetting for raw read counts. I am planning to use median method of normalization over TMM.  I want to subset for >10 counts and it should be present in atleast ...
written 3.6 years ago by myprogramming20160
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... Hi, I am not quite clear about the normalization in edgeR. I am not seeing any change in the actual read counts. They are same numbers except filtered for >10 reads, library size is reduced and norm.factor is 1. Could you please comments on this? Codes: x<-read.delim("counts.txt",header=T ...
written 3.6 years ago by myprogramming20160 • updated 3.6 years ago by Gordon Smyth38k

#### Latest awards to myprogramming2016

Popular Question 2.3 years ago, created a question with more than 1,000 views. For summaries featureCounts output for egeR
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Normalization in edgeR
Popular Question 2.3 years ago, created a question with more than 1,000 views. For threshold to filter lowly expressed genes

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