User: Noah Dowell

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Noah Dowell410
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Posts by Noah Dowell

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Comment: C: Trouble creating a ShortReadQ object and using writeFastq
... Thank you Martin! Once again you caught a simple mistake I was making with regards to using the wrong argument (filepath instead of file). Changing it to 'file' allowed writeFastq to work but then reading the newly written fastq file threw the same "line error" when I tried to read it in with readF ...
written 6.7 years ago by Noah Dowell410
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Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
... Hello All, I am trying to do some preprocessing quality analysis on PacBio reads. To make any plots of quality score or nucleotide frequency one should only look at reads of the same length. One output from PacBio filtering of the raw data is a FASTQ file. The nature of the PacBio reads is that t ...
preprocessing shortread written 6.7 years ago by Noah Dowell410
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Trouble creating a ShortReadQ object and using writeFastq
... Hello All, I am trying to do some preprocessing quality analysis on PacBio reads. To make any plots of quality score or nucleotide frequency one should only look at reads of the same length. One output from PacBio filtering of the raw data is a FASTQ file. The nature of the PacBio reads is that t ...
preprocessing shortread written 6.7 years ago by Noah Dowell410 • updated 6.7 years ago by Martin Morgan ♦♦ 23k
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Comment: C: Rsubread package not available? Warning resolved
... TIm, Thanks for providing your experiences on using different aligners. I used R/Bioconductor for tiling and expression arrays as a grad student but now I am using next generation sequencing as a postdoc so I am getting up to speed with some new packages like Rsubread. Yes, I have the Xcode devel ...
written 7.9 years ago by Noah Dowell410 • updated 7.9 years ago by Gordon Smyth38k
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Comment: C: Rsubread package not available? Warning resolved
... Dear Wei, Thanks for your response. I was going to use Rsubread with a small(ish) data set on a desktop with a little more memory than the standard laptop. I like the approach behind Rsubread and I wanted to do some comparisons with other aligners on small data sets before making a choice. Of co ...
written 7.9 years ago by Noah Dowell410 • updated 7.9 years ago by Gordon Smyth38k
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Rsubread package not available?
... Hello All, I am trying to use the Rsubread package which is supposedly available but I am getting the following warning message. Thanks for your help. Best, Noah ``` > source("http://www.bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("Rsubread") B ...
rsubread biocinstaller written 7.9 years ago by Noah Dowell410 • updated 7 weeks ago by Gordon Smyth38k
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Answer: A: problem using affxparser on MacOSX
... Hello Fabrice, Thanks for the response. It seems you are right; I did get affxparser installed using the following: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("affxparser", type = "source") And now Starr is working too. Have a ...
written 7.9 years ago by Noah Dowell410
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Comment: C: problem using affxparser on MacOSX
... Hello Fabrice, I was having the same problem using the Starr package(depends on affxparser) and tried the following: To re-install affxparser alone using: > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > update.packages("affxparser", repos=bi ...
written 7.9 years ago by Noah Dowell410
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Comment: C: readCelFile function in Starr is crashing R
... Hello Kasper, I have tried your suggestions but I am not having much luck. It very well may be my fault but any additional help is appreciated. 1. I went to CRAN this morning and downloaded R but I am not seeing any updates past the 10-31-2011 version. Are you suggesting I move to a developer ...
written 7.9 years ago by Noah Dowell410
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Answer: A: Extracting top upregulated genes from Limma analysis
... Hello Casper, This is from memory so double check it but the following should work: results <- decideTests(fit2, method="global") up <- which(results[,1] == 1) upGenes <- fit2[up, ] upTable <- topTable(upGenes[,4], number = 50, adjust.method= "BH", sort.by="p") The decideTests functi ...
written 8.6 years ago by Noah Dowell410

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