User: ctl

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ctl0
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Posts by ctl

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Answer: C: DESeq2/tximport 'duplicate rownames not allowed' error
... Please ignore this. I found the mistake.  My metadata table had some repeated samples, after removing them everything worked just fine.  Thanks!  ...
written 13 months ago by ctl0
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DESeq2/tximport 'duplicate rownames not allowed' error
... Hi,  I have used Salmon to quantify some 126 samples using the mouse ensembl reference cDNA transcriptome. Then I tried to obtained  abundance values using tximport as follows: txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM", ignoreTxV ...
deseq2 tximport written 13 months ago by ctl0
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Read Illumina BeadArray control table into Limma
... Hi I'm trying to analyse some microarray data using Limma. The sample probe data is in GenomeStudio format and Limma read this nicely, but the control probes are in a table.  When I load this into Limma I got an error:  Error in readGenericHeader(fname, columns = expr, sep = sep) :  Specified col ...
microarray limma transcriptome written 3.0 years ago by ctl0 • updated 3.0 years ago by Gordon Smyth38k
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Answer: A: tximport all(file.exists(files)) is not TRUE
... Hi! Yes, that helped me to solve the problem. There was an issue with my sample file.  Thanks a lot for the support.  ...
written 3.0 years ago by ctl0
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tximport all(file.exists(files)) is not TRUE
... I'm posting this error here to have a clearer idea of what's going on.  I'm running tximport using my own dataset and following and modifying the instructions on the vignette. But I have found an issue and I can't get around it.   I have specified my working directory under the variable dir as fo ...
rnaseq R bioconductor tximport written 3.0 years ago by ctl0

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For tximport all(file.exists(files)) is not TRUE

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