How to remove GRUB from Ubuntu-Vista dual boot

Preface: when it comes to installing operating systems I am a script kiddie. Every time I find a solution to some problem I am so happy I want everyone to know. This is why I am publishing this post, although, as you will see, all of the merit goes to a “mysterious” user of askubuntu, anwar.
I was in a situation in which I had an old laptop with a small partition reserved for Linux Ubuntu and a large one for windows.
I decided to give the PC to my mum, who will never use Ubuntu, and she likely would have troubles in managing dual boot.
Thus, I set out to remove grub.

Note: I do not have any install disk, nor recovery disk. Maybe I had them, once, not sure. In case you have a recovery disk, then things are easier.

Luckily enough, I found the answers here on askubuntu (answer by Anwar):

I repost it (with minor modification), in case somenone else may need it.

1) First download bootsect.exe from here into the Download directory (Warning the download will bring you through some redirection, but at the end you will get the program).
2) Rename the file to bootsect.exe (the name should be _Getintopc.com_bootsect.exe)
3) press the windows key, type cmd.exe and on the result (The command prompt) start it as an “Administrator” by right clicking on the cmd icon, and select Run as Administrator.
4) In the new cmd.exe window, cd to your download directory. for example cd C:\Users\Lalu Patel\Downloads. _assuming your user name is “Lalu Patel”.
5) Then enter this command. bootsect.exe /nt60 ALL /force /mbr.
6) Restart your system to see that, Windows is automatically loading without grub.

At this point, if you need to resize your partition, just go to askubuntu and follow the instructions

Visualize KEGG pathway and fold enrichment

As a useful note to self, I paste here an easy example on the use of the pathview package by Weijun Luo to plot the log fold change of gene expression across a given KEGG pathway. This example is on Vitis vinifera (as the prefix vvi can suggest), but the approach is general.
Basically, you just need to feed pathview the pathway argument and a argument. In this case, is a named vector, with names being the (entrez) gene names, and the value is the log Fold Change.
I selected a pathway for which KEGG has a nice representation, you might not be so lucky!


The result should be something like this:

Perform pairwise Wilcoxon test, classify groups by significance and plot results

This post is the result of work performed in collaboration with my colleague Eleonora Paparelli (who actually did most of the work!). We wanted to compare several distributions using Wilcoxon test and summarize results (i.e. indicate the comparisons showing significant differences).
R base includes pairwise.wilcox.test to perform Wilcoxon rank sum test between all pairs of samples in a study.
A common way to represent significance in pairwise comparisons is the use of letters. Samples sharing a letter are not different from each other. Samples not sharing letters are different.
Library multcompView in R can take a square matrix of p-values and return letters for all samples.
Sadly enough, pairwise.wilcox.test returns a triangular matrix, so I had to write a small function – named – to take the output of pairwise.wilcox.test and convert it in a suitable input for the multcompLetters function of multcompView.
Now we can easily plot the distributions as box plot and add the letters as text.


for(ext in 1:length(cn))
 for(int in 1:length(rn))
 if([row.names(x)==rn[int],colnames(x)==cn[ext]])) next


pp<-pairwise.wilcox.test(full[,1], full[,2], p.adjust.method = "none", paired = FALSE)

boxplot(full[,1] ~ full[,2],ylab="Something nice",names=c("Set 1","Set 2","Set 3"),ylim=c(min(full[,1]),0.3+max(full[,1])))

Reading large data tables in R

Ok, I confess.

Until yesterday I was one of those still trying to read large data tables using read.table.

Then, I came across this thread in stackoverflow and I saw the light.

Since I noticed that a lot of people still struggle with read.table I decided to write this very brief post.

Imagine that you have your large file named “mylargefile.txt”. Then all you have to do is the following.


I promise I’ll never go back to read.table again!

Summarize content of a vector or data.frame every n entries

I imagine that the same result can be achieved by a proper use of quantile, but I like to have an easy way to obtain summary statistics every n entries of my dataset be it a vector or data.frame.

The function takes three parameters: the R object on which we need to obtain statistics (x), how many entries should each summary contain (step, defaulting to 1000), and the function we want to apply (fun, defaulting to “mean”).

Then, it’s all about using aggregate.

The present version incorporates useful comments by pat and ap53! <- function(x,step=1000,fun="mean")
n <- NROW(x)
x <- data.frame(group,x)
x <- aggregate(x,by=list(x$group),FUN=fun)
x <- x[,-c(1,2)]

Example application and result for a data.frame:

          X1        X2        X3        X4        X5        X6        X7
1  0.5081756 0.5206011 0.4972622 0.5060707 0.4907807 0.5063138 0.4982252
2  0.5014300 0.5093051 0.5015310 0.4718058 0.4931249 0.4882382 0.5084970
3  0.4994759 0.4979546 0.4964157 0.5138695 0.5018427 0.5228862 0.4980824
4  0.4970300 0.4953163 0.4954068 0.5157935 0.4770471 0.5000562 0.4960250
5  0.5118221 0.4967686 0.5114420 0.4945936 0.5016019 0.5003544 0.5016693
6  0.5026323 0.4995367 0.5003587 0.4970245 0.4992188 0.4993896 0.4873300
7  0.4911944 0.5081578 0.4858666 0.4974576 0.4864710 0.5022401 0.5058064
8  0.5050684 0.5021456 0.4970707 0.4829222 0.4980984 0.4901941 0.5053296
9  0.4910359 0.4883865 0.4915000 0.4984415 0.4941274 0.4933778 0.4964306
10 0.4832396 0.4986647 0.5017873 0.5008766 0.4952849 0.5036030 0.5084799
          X8        X9       X10
1  0.5052379 0.4906292 0.4916262
2  0.5074966 0.5117570 0.5183119
3  0.4988349 0.5029704 0.5077726
4  0.4889516 0.5066026 0.5078195
5  0.5068717 0.4988389 0.5018225
6  0.5010366 0.4870614 0.4827767
7  0.5148197 0.5083662 0.5037901
8  0.4979452 0.5273463 0.4944513
9  0.5130718 0.5061075 0.5058208
10 0.4896030 0.4911127 0.4956848

And for a vector

 [1] 0.4914789 0.4908839 0.4951939 0.4928015 0.4911908 0.4994735 0.4947729
 [8] 0.5058204 0.5026956 0.5018375

A biologist’s guide to linux “screen”

I write here a very concise guide to linux screen (ok, I assume you know something about linux, even if you are a biologist…).
It takes five minutes to learn and you can live with it for all of your life. Trust me, I’m a biologist!

Why screen?
If you work on a remote server and there is an interruption of your internet/LAN connection, all you were doing is gone. Screen prevents you against these data losses.
How does it work?
Simple. To create a screen or resume an existing screen you can use the ever useful command
screen -dR

Then, when you are in screen you can do all your work ignoring you are in screen except that you have a series of screen commands that help you create several screens inside the same terminal and also move around them.
Any screen command starts pressing at the same time ctrl-a (yes, even in mac).
AFTER pressing ctrl-a you can press one of the following letters:
c: create an additional screen
n: move to next screen (if existing)
p: move to previous screen (if existing)
d: detach screen

The only command that needs not be preceded by ctrl-a is exit. If you type exit inside screen you will quite screen and erase it from memory (so do not type exit if you have unsaved work).

Restituire dignità alla wi-fi fastweb

Ammettiamolo, ultimamente la rete fastweb non è il massimo.
So di svariate persone che si riducono ad usare la chiavetta per navigare… da casa.
Anche la mitologica “riqualifica della linea”, la prima opzione che immancabilmente fastweb propone, ultimamente non dava risultati.
Stavo veramente meditando a quale nuovo operatore affidarmi quando ho avuto un lampo di genio (ebbene sì, io non ho culo, ho lampi di genio) e mi sono imbattuto in una serie di post che suggerivano di cambiare il canale del wireless.
Nonostante io sappia a malapena cambiare il canale della TV (strumento che da decenni non possiedo più) ho deciso di cimentarmi in questa impresa.
Con un po’ di colpi di c… ehm di genio, sono riuscito a farlo. Scrivo qui la mia avventura a imperitura memoria e affinché gli altri poveri sfigati come me vittime della lentezza del wi-fi fastweb vi trovino consolazione e – magari – la salvezza, come è capitato a me.

Allora, un po’ rocambolescamente ho trovato questa pagina di fastweb in cui si accede alla configurazione del wifi di fastweb (ovviamente bisogna effettuare il login):

Si presenta una pagina, nelle cui prime righe c’è un link un po’ mimetizzato che io però ho evidenziato con una freccia rossa


Una volta cliccato, si aprirà un pop-up nel quale ci sono vari settaggi. Basta cercare “Modifica canale wi-fi” e cambiare il numero.


Io, dall’alto delle mie competenze informatiche, ho cambiato a caso.
Ha funzionato.
Auguro anche a voi la stessa fortuna.