User: cstrato

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cstrato3.9k
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Posts by cstrato

<prev • 442 results • page 1 of 45 • next >
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Answer: A: [xps] Problems building scheme for DroGene 1.1 ST arrays in xps
... Perl Script PART 2: #------------------------------------------------------------------------------# # append/replace control->affx lines to probeset annotation file out_annot_ps #------------------------------------------------------------------------------# print("appending control->affx ...
written 13 days ago by cstrato3.9k
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Answer: A: [xps] Problems building scheme for DroGene 1.1 ST arrays in xps
... Perl Script PART 1: ###### BEGIN perlscript "DroGene11_update_AFFX.pl" ###### #!/usr/bin/perl # #------------------------------------------------------------------------------# # Perl script to update AFFX controls of DroGene-1_1-st annotation files na36 # # Copyright (c) 2012-2018 Christian Stra ...
written 13 days ago by cstrato3.9k
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Answer: A: [xps] Problems building scheme for DroGene 1.1 ST arrays in xps
... PART 2: Here is my code and the corresponding correct output: library(xps) libdir <- "/Volumes/T3Data/CRAN/Workspaces/Drosophila/DroGene-1_1-st" anndir <- "/Volumes/T3Data/CRAN/Workspaces/Drosophila/DroGene-1_1-st-v1-na36-dm3-transcript-csv" anndir2 <- "/Volumes/T3Data/CRAN/Workspaces/D ...
written 13 days ago by cstrato3.9k
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Answer: A: [xps] Problems building scheme for DroGene 1.1 ST arrays in xps
... Hi Chris, NOTE:  My reply seems to be tooo long, only 5000 characters are allowed, so I divide my answer into different parts!! PART 1: As I have already mentioned the missing AFFY controls in the probeset and transcript annotation files are an old problem. In 2012 it took me many weeks until Aff ...
written 13 days ago by cstrato3.9k
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Comment: C: [xps] Problems building scheme for DroGene 1.1 ST arrays in xps
... Hi Chris, This is an old problem of Affymetrix. Sometimes they do not add all AFFX controls to the annotation files or had controls in the annotation files which were missing in the pgf-file.  Usually I have asked Affymetrix DevNet to add the controls. I will check my old records to see if there i ...
written 14 days ago by cstrato3.9k
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Comment: C: unable to load xps
... Hi Ashish, I am glad to hear that you could finally install xps. It is strange that you had to use the source code from the development version, since the relevant changes are also available in the release version. I have no experience with RStudio, and usually I recommend to run xps from xterm. ...
written 23 days ago by cstrato3.9k
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Comment: C: unable to load xps
... Hi Ashish, Can you tell me how you have compiled and installed ROOT? On Mac (BSD Unix) you have to do after make: $ . bin/thisroot.sh   (the first symbol is a dot) As far as I remember you need to run this command on Linux, too. At least on Mac this command makes sure that the environment variab ...
written 23 days ago by cstrato3.9k
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Comment: C: unable to load xps
... Hi Ashish, Please try the following in '.bashrc': 1, delete 'export DYLD_LIBRARY_PATH' which is only needed for Mac    delete 'export LD_LIBRARY_PATH'    Now test if xps does work.      If there are still problems: 2, delete also 'export ROOTSYS' In principle you should no longer need to define $ ...
written 26 days ago by cstrato3.9k
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Comment: C: unable to load xps
... This means still that xps does not find ROOT. - Please run the ROOT tutorials to see if libGui.so does work.   You find 'demos.C' in directory root/tutorials so you need to 'cd' there. - How does the '.bashrc' file in your home directory look like? - Does 'R CMD INSTALL xps' install xps?   See th ...
written 26 days ago by cstrato3.9k
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Comment: C: unable to load xps
... Hi Ashish, As usual, the error indicates that xps does not find ROOT. For this reason I need to know the following: - Did you download ROOT from: https://root.cern.ch/content/release-53436 - Did you download and compile the source code yourself?   (This is the option I recommend) - Or did you i ...
written 26 days ago by cstrato3.9k

Latest awards to cstrato

Scholar 20 months ago, created an answer that has been accepted. For A: [XPS]Installation of ups package in macOS Sierra
Scholar 2.5 years ago, created an answer that has been accepted. For A: MAS5 algorithm in mas5() function of xps function when process Human Gene 1.0 ST
Scholar 3.5 years ago, created an answer that has been accepted. For A: HuGene 2.0 ST CDF files and xps
Scholar 4.1 years ago, created an answer that has been accepted. For A: HuGene 2.0 ST CDF files and xps
Centurion 4.1 years ago, created 100 posts.

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