User: lm795

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lm7950
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Posts by lm795

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... It seems that answering no to that question bypasses the issue. I still had to answer yes to the questions downstream. Many thanks for that suggestion, it bypasses installing more stuff on top of OSX. ...
written 5 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Hi again James, still unable to install affycoretools with the instructions above. The "remotes" package seems to be installed but I don't see it under "Packages" in RStudio. The message from attempting to install "affycoretools" is below. Many thanks for your help. > BiocManager::instal ...
written 5 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks, I will follow your advice Martin. I run RStudio on Macs and keep my projects in Dropbox so will have to upgrade a couple of computers.. ...
written 6 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Something like that. I am on Macs so I guess I must use Homebrew ...
written 6 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks, that's useful. I wish there was a way to upgrade R from the command line, like "sudo apt-get update"... ...
written 6 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks for that! I am right to conclude that I only need to upgrade BioC on the 30th (and not R). I am on R version 3.5.1 ...
written 6 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks for the speedy reply James, perhaps I am the only punter using pd.drogene.1.1.st but these are much cheaper than RNAseq. I might try GitHub once I learn how to install a library from there.. ...
written 6 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Hi James, it's me again. I noticed that this feature is still not fixed. Are you planning to fix it anytime soon? I was going to add my script to GitHub but it would be more useful if annotateEset was working for these arrays... All the best, Miguel ...
written 6 days ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Thanks for the extra advice. I am not familiar with that package so will have a look. I used BioMart before, as I can use that DB for orthologue mapping. I sometimes want to query Ingenuity Pathway Analysis DB (QIAGEN) and they only hold mouse and human data. Whenever I load fly gene IDs I get fairl ...
written 6 months ago by lm7950
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... Fair point James, I agree. I can always query BioMart to retrieve the extra annotation. Thanks again for your help! ...
written 6 months ago by lm7950

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