User: Akira Imamoto

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Posts by Akira Imamoto

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Comment: C: Any trick to use "tximport" for converting a simple read count table ?
... Sorry! I found a solution myself for the input for DESeqDataSetFromMatrix(). Simple matrix didn't work, but adding rownames to a count-data-only table solved it. tablex=as.matrix(table[,c(5:12)]) ## column3 is "RefSeqID";columns 5-12 are raw counts rownames(tablex)=table[,3] Thanks for taking tim ...
written 2.7 years ago by Akira Imamoto0
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Comment: C: Any trick to use "tximport" for converting a simple read count table ?
... Thank you very much for quick reply. I was trying to find a solution to my problem with DESeqDataSetFromMatrix(). I tried but it did not take a matrix as you can see below. Only way so far was to put count columns without the row name column (in this case Symbol). What am I doing wrong? > dataf ...
written 2.7 years ago by Akira Imamoto0
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Any trick to use "tximport" for converting a simple read count table ?
... Hi,  I'm hoping to use "tximport" to convert an RNA-Seq count data file for downstream analysis such as DESeq2. But I got an error as you can see below. I think everything I have is current (R3.3.1 etc). Any input will be much appreciated !!  > datafileName <- "test.txt"  ## Replace the fil ...
tximport written 2.7 years ago by Akira Imamoto0 • updated 2.7 years ago by Michael Love23k
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Comment: C: Error to convert a DGEList to DESeqDataSet in DEFormats
... Thanks for your reply! I get the same error in my Mac, Ubuntu, or Windows...  Following is a copy of one of such sessions, including sessionInfo() output.     R version 3.3.1 (2016-06-21) -- "Bug in Your Hair" > gr=rep(c("untreated","OHT"), 4) > dge=DGEList(counts = rawcounts[, 4:11], ge ...
written 2.7 years ago by Akira Imamoto0
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Error to convert a DGEList to DESeqDataSet in DEFormats
... I get an error message when converting a DGEList (edgeR) to DESeqDataSet (DESeq2) in DEFormats. Following is a part of the R window that reported an error. Please let me know if there is a remedy for this problem.  Thanks! > gr=rep(c("untreated","OHT","untreated","OHT","untreated","OHT","untrea ...
edger deseq2 deformats written 2.7 years ago by Akira Imamoto0
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Comment: C: QLF or LRT in edgeR for paired sample designs?
... Thank you very much for the clarification as well as the links for the previous posts. Yes, it is easy to swap them. When I compared them yesterday, I found that glmQLFTest is more conservative than glmLRT in general for our RNA-Seq experiments. My question came up as I found one of the three sets ...
written 2.7 years ago by Akira Imamoto0
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QLF or LRT in edgeR for paired sample designs?
... This may be a naive question, but I am wondering which, glmFit/glmLRT or glmQLFit/glmQLFTest, I should use for DE gene analysis in paired designs using edgeR. In the edgeR Users Guide (rev 20.4.2016),  glmFit/glmLRT is used in Chapter 3.4.1 and 4.1 for paired designs, whereas glmQLFit/glmQLFTest is ...
edger glm paired samples ql f-test lr-test written 2.7 years ago by Akira Imamoto0 • updated 2.7 years ago by Aaron Lun23k

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For QLF or LRT in edgeR for paired sample designs?

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