User: Devon Ryan

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Devon Ryan200
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Posts by Devon Ryan

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Answer: A: perspective on differential expression counting - unmapped reads?
... You can just remove those lines (in fact, that's what DESeq2 does internally), they'll just needlessly increase the number of tests performed. ____________________________________________ Devon Ryan, Ph.D. Email: dpryan at dpryan.com Tel: +49 (0)178 298-6067 Molecular and Cellular Cognition Lab Ger ...
written 5.8 years ago by Devon Ryan200
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Comment: C: DEXSeq update
... That's a warning, not an error and you can likely ignore it. As Simon alluded in his earlier reply, the script expects mates in a pair to follow one another. When they don't, the warning you observed is issued. With tophat, this can occur when (1) you don't specify --no- mixed or (2) you specify --f ...
written 5.9 years ago by Devon Ryan200
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Answer: A: DEXSeq update
... It would be helpful if you reported the actual error messages. ____________________________________________ Devon Ryan, Ph.D. Email: dpryan at dpryan.com Tel: +49 (0)178 298-6067 Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bon ...
written 5.9 years ago by Devon Ryan200
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Answer: A: DEXSeq Paired-end analysis (new issues)
... Hi Margaret, It's expecting a SAM file, not a BAM file: samtools view -h ahBC010.sam.bam | dexseq_count.py -p yes -s no hs71.gff - ahBC010.counts Note that - specifies reading from the standard input rather than a file. Cheers, Devon ____________________________________________ Devon Ryan, Ph.D ...
written 5.9 years ago by Devon Ryan200
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Comment: C: GC counts
... FYI, this ended up getting discussed on biostars (http://www.biostars.org/p/82308/) and the context turned out to be RNAseq normalization (the question ended up being answered there as well). ____________________________________________ Devon Ryan, Ph.D. Email: dpryan at dpryan.com Tel: +49 (0)178 ...
written 5.9 years ago by Devon Ryan200
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Answer: A: microarray outlier detection
... To expound on what Peter Langfelder wrote, some people get in the unwise practice early in their careers of removing what the think are outlier datapoints/samples simply because it makes their data cleaner. This is a really bad idea because you end up chronically underestimating biological variabili ...
written 6.0 years ago by Devon Ryan200
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Answer: A: DEseq for paired samples
... Hi Prabhakar, The general method you're looking for is to add "patient" (or whatever term you prefer) as a factor in your design. So, if you denote tumor/normal by a factor called "status": counts ~ status + patient would likely be the formula you want. You could also allow an interaction if it m ...
written 6.0 years ago by Devon Ryan200
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Answer: A: basic query to make groups ..
... You're telling R that "k" is just a character in the grep pattern. Try: grep(sprintf("^%i.[0-9]",k), x)) -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Laboratory for Molecular and Cellular Cognition German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn Germany On W ...
written 6.0 years ago by Devon Ryan200
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Answer: A: about running gsva on mac
... Are you running this in R.app or R from the terminal? If the former, try running things from the terminal and see if the problem persists. Some parallel computing related packages (e.g. doMC) will give this error in a GUI. Devon ____________________________________________ Devon Ryan, Ph.D. Email: ...
written 6.0 years ago by Devon Ryan200
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Answer: A: Trimming of partial adaptor sequences
... Hi Sean, Have you tried just using a read trimmer, such as trim_galore or trimmomatic? That would seem much easier than rolling your own solution in R. Cheers, Devon ____________________________________________ Devon Ryan, Ph.D. Email: dpryan at dpryan.com Molecular and Cellular Cognition Lab Ger ...
written 6.1 years ago by Devon Ryan200

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