Visualisation of proteomics data using R and Bioconductor

https://www.bioconductor.org/packages/release/data/experiment/vignettes/RforProteomics/inst/doc/RProtVis.html

Looking up Uniprot resources in Bioconductor

https://bioconductor.org/packages/release/bioc/html/UniProt.ws.html


see also:
http://mygene.info/mygene-included-in-bioconductor-3-0-release/

This is also an interesting resource:
https://www.bioconductor.org/packages/release/data/experiment/vignettes/RforProteomics/inst/doc/RProtVis.html

Learned more from W3

For information and advice about coding, W3 is a great resource.
I just improved my blog using the information about formatting tables:
http://www.w3schools.com/html/html_tables.asp

Converting PDF to text...

I want to try scraping some data from PDF reports....
The recommendation seems to be to use pdftotext.

This pages tells me how to install:

• http://superuser.com/questions/286961/pdf-to-text-convertor

It's UNIX command line stuff....

brew install xpdf

or I could have tried:

brew install poppler

I don't know yet if there is a difference...

I followed the first one and put in the command 

pdftotext your_pdf_file.pdf

and it's fast on the document, I used....

It works but for a small number of documents (say 10), it's nearly easier just to download each document, copy and paste....

manipulating csv files...

A colleague used Unix to manipulate a csv file.
It was very large so importing it into R or opening in Excel would have causes some problems.

the command used was

• cut - http://stackoverflow.com/questions/7857090/awk-extract-specific-columns-from-delimited-file

perl was also used directly from the unix prompt to remove everything starting with a hash tag #

Useful addition to the data munging world!

Principal Component Analysis and other tools...

http://stats.stackexchange.com/questions/65692/how-to-visualize-what-canonical-correlation-analysis-does-in-comparison-to-what/65817#65817

http://stats.stackexchange.com/questions/95038/how-does-factor-analysis-explain-the-covariance-while-pca-explains-the-variance/95106#95106

http://stats.stackexchange.com/questions/94048/pca-and-exploratory-factor-analysis-on-the-same-data-set/94104#94104

Time to update R...

When you get one of these:

Warning message:
package ‘dplyr’ was built under R version 3.1.2 


it's probably time to check the version of R, your using and probably time to update it too!

Type
> version

into the Console of R-studio and it will tell you what version you have currently..

I just updated R and got this response:

platform       x86_64-apple-darwin13.4.0   
arch           x86_64                      
os             darwin13.4.0                
system         x86_64, darwin13.4.0        
status                                     
major          3                           
minor          2.2                         
year           2015                        
month          08                          
day            14                          
svn rev        69053                       
language       R                           
version.string R version 3.2.2 (2015-08-14)
nickname       Fire Safety