User: Bio Sam

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Bio Sam60
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10 years, 4 months ago
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13 years, 1 month ago
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b*****@gmail.com

Posts by Bio Sam

<prev • 6 results • page 1 of 1 • next >
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Answer: A: siggenes: sam2html + affymetrix zebrafish
... Thanks for the suggestion, disabling refseq seems to fix the error: sam2html(sam.out.rma, delta.rma, "sam_out_rma.html", cdfname="zebrafish", refseq=F) Sam On Wed, Jun 10, 2009 at 1:12 AM, Holger Schwender wrote: > Hi Sam, > > no, I actually have no idea. It seems that one of public rep ...
written 10.4 years ago by Bio Sam60
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siggenes: sam2html + affymetrix zebrafish
... Hi, I recently updated to R2.9 and after reinstalling Bioconductor packages have run into the following error with annotations and the sam2html function in siggenes: "Error in FUN(X[[1L]], ...) : unknown repository 'GB' " After running the following code: > library(siggenes) > sam.out.rma ...
zebrafish written 10.4 years ago by Bio Sam60
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Answer: A: How do you keep track of your analyses
... I like to keep a main working directory, then make a sub directory for each project with a directory name containing date, contact name, and project title. This makes it easy to see when I started a project, and keeps things sorted chronologically: /working /working/2008-02-29-Contact_project Ins ...
written 11.1 years ago by Bio Sam60
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zebrafish annotation
... Hi Marc, and the Bioconductor mailing list, I do a fair amount of work with the Affymetrix Zebrafish platform, but the recent move to .db annotation files seems to have left zebrafish behind. From what I've read in previous posts to the Bioconductor list, the new .db annotation packages are not ea ...
annotation zebrafish written 11.1 years ago by Bio Sam60 • updated 11.1 years ago by Marc Carlson7.2k
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Comment: C: Problems installing bioconductor on ubuntu
... Hi Rebecca, as a big fan of Ubuntu and Bioconductor, I've gone through a number of installs, and run into many similar headaches. As Steve pointed out, you are missing gcc and associated libraries, which you can get from build-essentials. This will get many packages working, but I typically als ...
written 11.3 years ago by Bio Sam60
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Comment: C: Problem obtaining QC statistics from 'simpleaffy'
... Hi Greg, I had a similar problem when trying to run the affy qc stuff on barley. After some digging I found that the necessary entries were not included for the barley chip in the packages data files "qc.probes.tab", "alpha.tab", and "spikes.tab" which are located in "/usr/local/lib/R/site-library/ ...
written 13.1 years ago by Bio Sam60

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