aracne in R using minet package

Question

[nazaninhoseinkhan]

Hi,

I am trying to work with "minet" package in R. I have to import a large table of expression values in R. in minet tutorial it has said that data must be entered as data frame using this command: data(syn.data). I do not know in which format I have to import my data or what file extension should I use.

Can anybody suggest me any solution?

Regards
Nazanin

[komal.rathi]

That is just an example to load the sample dataset for demonstrating the package.

You can use read.table or read.delim to read in your file/data.

Answer 1

[nazaninhoseinkhan]

Hi

My problem was solved. The input I used was a compendium of gene expression data, i.e. the rows were gene names and the columns correspond to samples. Before using minet I had to transpose this matrix in excel, because minet needs genes as columns and samples as rows. After reading this table via read.table command, minet works properly.

Let me know if you have any question

Good luck

Nazanin

[zizigolu]

Hi Nazanin,

Do you mean from aracne, ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks)? If so, can u please help me launch it in windows?

Thank you

[nazaninhoseinkhan]

Hi Sara,

You must have R installed on your computer. Then you have to install "minet" package in the R. You can get it from Bioconductor.

You can find instruction for its running (very simple) from "minet package tutorial": http://www.bioconductor.org/packages/release/bioc/manuals/minet/man/minet.pdf

Good luck

[zizigolu]

Thanks a lot Nazanin, I already installed R 3.2 and downloaded "minet" package. Can I ask you my question about preparing input file? Because I have not prepared excel file yet.

[nazaninhoseinkhan]

Sure,

Normal gene expression data sets, such as affymetrix cel files represent gene names in rows (I mean the first column) and conditions in columns. You need to transpose this table, i.e. gene names in columns and conditions in the rows.

Then using these two commands in R:

mim <- build.mim(syn.data,estimator="spearman")
net <- aracne(mim)

You can run aracne.

Good luck

[zizigolu]

You know Nazanin I am totally confused now. I opened R and typed mim <- build.mim(syn.data,estimator="spearman") but it said that Error: could not find function "build.mim" I installed java 8 and downloaded aracne from http://wiki.c2b2.columbia.edu/califanolab/download/ARACNE/aracne.zip, unzipped then based on manual doubled clicked on launch_aracne.bat file but no happen I saw also this file is just 1 kb. I am in Windows.

Even I installed geworkbench but I could not find where I can change the aracne MI or until I read a post by you about working with aracne in R.

Can you please help me more, I really need your help

[nazaninhoseinkhan]

It seems you are so confused. I have worked with geworkbench, minet and ARACNE itself in command line. I am so busy but I can help you more on Skype. Let me know when it is OK for you

[zizigolu]

Thanks a lot for your kindness

Yes you are right I am too confused and helpless at the time. I read in the manual that working with command line require access to cluster computing and some expertise. I searched for your email a lot but I could not find that. Now I am working with geworkbench because I know just a little bit about R. I am so eager to talk whenever possible for you

[nazaninhoseinkhan]

Hi Sara,

I think at 9:30 PM (Tehran time) is OK for me.

My skype id is: nazaninibb89

My email: [e-mail]

[zizigolu]

Hello Nazanin I am thankful for your attention. Excuse me if I replied with delay because of some problem.

Thank you for your email

Answer 2

[sedaghat.nafiseh]

You can see a sample code as below:

'data' is a matrix which each row corresponds to a prob and each column corresponds to gene.

mim <- build.mim(data,estimator="spearman")
net1 <- aracne(mim,eps=0.1)

[nazaninhoseinkhan]

Dear Nafiseh, Thanks, my problem was solved last week. I just had to use read.table command in R. The data matrix was itself in proper format. Thanks again for your consideration and Good luck Nazanin

[stroman05]

I am also learning minet for the first time. To start with where can I get the input datasets and what are its contents in rows and columns?