I opened Rstudio and typed
source ("http://bioconductor.org/biocLite.R") in console part but says that
A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
I have already installed R 3.2.0 and
2.15.0, and when I typed
biocLite() it said that:
BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/src/contrib
Then why warning yet?
Are you using RStudio? If so check to make sure it is that latest version. When I updated my R it was not very compatible with the older RStudio. Then I had to reinstall all my Bioconductor packages with the new R and RStudio versions.
Thank you alolex for your attention. I don't know how I know whether my Rstudio is the latest version or not.
May I ask another question which I got bad confused about specially with sporadic searching and tremendous pages.
I downloaded an array experiment (GSE33964), I am interesting in knowing which genes expressing in this experiment is correlated with my genes (genes involved in sterol biosynthesis pathway in citrus sinensis), something like Co-Expression Network Analysis using Pearson's correlation coefficient or another way. Do you think please my idea has any sense or I am wasting time? Especially I am fighting with R to process the data and I am just a beginner. If possible give me some advice.
Please post this as a new question as it is not related to the original question on this page. Also, if you could provide some more details about your data (time points, replicates, conditions etc) that would help answer your question.
With regards to the RStudio version you can type R.Version() to get the version information. When I do this in my RStudio I get the following output:
My data are like this:
About my Rstudio
OK, sorry, that was actually the R version info, which it looks like you are using the most current, but bioconductor is seeing your old version for some reason. Try the following few suggestions, and make sure you restart RStudio.
To see your RStudio version:
They actually just posted a newer version of RStudio a few days ago, 0.99.441 here: http://www.rstudio.com/products/rstudio/download/
So you could try to install that version, then try your bioconductor installation again. If that doesn't work, try installing bioconductor through a vanilla session of R in the terminal (Command Prompt on Windows I think)--don't go through RStudio.
Did the suggestions from @Deepak and @airan work? If you are still having problems it would help if you could post all your command line input and output up to the error you are getting.
Unfortunately tips from Deepak and Airan didn't work.
Looks like you are all up-to-date. Try installing Bioconductor and packages using the R --vanilla approach, then go back to using RStudio. If that doesn't work I'm not sure I have any other suggestions :( as I have a mac and not windows. You can post this problem to the Bioconductor forum (https://support.bioconductor.org), and they may be able to help. As a complete last resort you can always completely uninstall R and RStudio, then reinstall them and start from scratch. I hope you figure it out!
I opened cmd and typed
but said that:
Anyway I am thankful...
Thank you alolex I went through your tip (https://support.bioconductor.org/) and I could download my packages from this link: https://support.bioconductor.org/p/68201/#68206
Great! Thanks for letting me know the solution. I'm glad you found someone who could help and that you got it working :) I know how frustrating things like that are!
I typed, something is downloading
Bioconductor in particular is that "something" :) Glad to help.
After downloading finished, I closed Rstudio and opended again and typed
source("http://bioconductor.org/biocLite.R")and clicked Enter
It said in red that:
Mmm...that's weird. If you type
sessionInfo(), which R version do you have?
I have R 3.2.0
Sorry, I have to install package whenever I launch Rstudio?
OK. Take a look to these two posts, specially the first one, and check if you can fix the problems:
OK thanks :)