You have multiple options. I will advertise my own solution - install the package WGCNA, installation instructions at
http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/#cranInstall then you can use the function cp = corAndPvalue(t(genes), t(features)). You need to transpose both because the function expects variables in columns and samples in rows. This will give you a list whose components include 'cor' (matrix of the correlation values) and 'p' (matrix of the Student p-values). To get a matrix of the corresponding FDR, use fdr = apply(cp$p, 2, p.adjust, method = "fdr") Hope this helps, Peter On Thu, Jun 18, 2015 at 1:19 AM, Sarah Bazzocco <sarah.bazzo...@vhir.org> wrote: > This post was called "help" before, I changed the Subject. > Thanks for the comments. > Here the example: (I have the two lists saved as .csv and I can open them in > R) > > Sheet one- Genes (10 genes expression, not binary, meaured in 10 cell lines) >> genes > Genes Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5 > 1 KCNAB3 12.02005181 11.1400910 15.60381163 13.44151596 25.37161030 > 2 KCNB1 0.02457449 1.3028535 0.81538294 0.59318327 0.15332321 > 3 KCNB2 0.44791862 0.1060137 0.09864136 0.00000000 0.00000000 > 4 KERA 0.06090217 0.0000000 0.03352993 0.03634781 0.04190912 > 5 KGFLP1 0.02450101 0.0000000 0.00000000 0.00000000 0.00000000 > 6 KGFLP2 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > 7 KHDC1 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > 8 KHDC1L 2.31894450 2.8252262 5.29099724 7.44183228 1.94629741 > 9 KHDC3L 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > 10 KHDRBS1 0.00000000 0.0000000 0.00000000 0.00000000 0.00000000 > Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10 > 1 8.12373424 7.67506261 24.43776341 18.33244818 9.224225 > 2 4.18181234 1.65268403 5.98346320 1.51423807 0.000000 > 3 0.05857207 0.05945414 0.20733924 0.05830982 0.000000 > 4 0.00000000 0.00000000 0.07752608 0.01585643 16.664245 > 5 0.02563099 0.03902548 0.00000000 0.00000000 0.000000 > 6 0.00000000 0.00000000 0.00000000 0.00000000 0.000000 > 7 0.00000000 0.00000000 0.00000000 0.00000000 0.000000 > 8 8.56022436 7.50838343 7.17964645 3.28602729 0.000000 > 9 0.00000000 0.00000000 0.00000000 0.00000000 3.598534 > 10 0.00000000 0.03081180 0.00000000 0.00000000 2.600173 > > Sheet two - features (2 features(Growth rate,drug sensitivity for 10 cell > lines) >> features > Cell.line Cell.line1 Cell.line2 Cell.line3 Cell.line4 Cell.line5 > 1 Growth rate NA NA NA 51.41 NA > 2 Drug sensitivity 5.03 6.57 8 1.26 3 > Cell.line6 Cell.line7 Cell.line8 Cell.line9 Cell.line10 > 1 41.33 26.76 24.19 NA NA > 2 1.40 1.88 1.33 5.05 9.12 > > What I found: > corr.test {psych} > corr.test(x, y = NULL, use = > "pairwise",method="pearson",adjust="BH",alpha=.01) > --> I adjusted the original command to what I need (BH insted og holm) and > alpha=.01 insted of 0.05. > > I would be very happy, if someone could show me how to use this command, in > particular how to refer as x and y to the two sheets I have (Genes and > Features). I would take it from there. > > Thanks a lot in advance. > > Sarah > > > > > > > ----- Original Message ----- > From: "Rainer Schuermann" <rainer.schuerm...@gmx.net> > To: "Sarah Bazzocco" <sarah.bazzo...@vhir.org> > Sent: Thursday, 18 June, 2015 8:14:56 AM > Subject: Re: [R] help > > > > Hi Sarah, > > > > Not an answer to our question but a piece of well intended advice: > > > > 1. Don't post HTML but plain text. Not only that people will tell you this in > a sometimes not very friendly manner - using HTML actually does make posts > illegible in this mailing list. Code, and R _is_ code, is always plain text. > > > > 2. Don't pose an abstract problem - this looks too much like "Can you please > do my work for me". Show us what you have tried already, and people will > happily jump in and provide their thoughts and advice. > > > > 3. Always make sure that you ave a reproducible example in your mail, and a > set of data of the same type and structure you are using - ideally using > dput(). > > > > See further advice here > > > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > and here: > > > > http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example > > > > For your problem, R has an immense wealth of ideas and solutions. > > > > Rgds, > > Rainer > > > > > > > > On Wed June 17 2015 16:57:24 Sarah Bazzocco wrote: > >> > >> Hello, > >> > >> � > >> > >> I am a R-beginner and I need some help.�The question is very simple: I need >> to do a pearson correlations (r,p-value and FDR with BH) from an Expression >> array (with several thousand genes for lets say 20 cell lines)�with some >> features of those cell lines. > >> > >> > >> > >> My problem I have is the organization of the excel sheets and how to >> introduce the data into R and run the script. I though the easiest and more >> organized for me would be two expcel sheets: > >> > >> 1- Only Expression data (in rows the�genes and in colums cell lines) > >> > >> 2- Only the features (In row the features (e.g. a) growth rate, b) >> sensitivity to some drugs) and in columns the cell lines). > >> > >> > >> > >> -->That would creat both sheets with 20 colums. > >> > >> > >> > >> Now I would like to get a correlation of the gene 1: the expression of all >> lines with the growth rate. > >> > >> the same for gene2... and soforth. I sould obtain as many r,p and BH(FDR) as >> genes there are. > >> > >> the same I would need to do for the sensitivity... and so on. > >> > >> > >> > >> Do you think this is doable? I am not at all a bioinformatic expert, so all >> help is very welcome. > >> > >> > >> > >> Thank you very much! > >> > >> > >> > >> Kind regards, > >> > >> > >> > >> Sarah > >> > >> > >> > >> > > > > -- > > > Sarah Bazzocco, PhD student > Group of Molecular Oncology, > CIBBIM-Nanomedicine, > Vall d'Hebron Hospital Research Institute, > Passeig Vall d'Hebron 119-129, > Barcelona 08035, Spain. > Tel: +34-93-489-4056 > > Fax: +34-93-489-3893 > Email: sarah.bazzo...@vhir.org > > > > -- > > > Sarah Bazzocco, PhD student > Group of Molecular Oncology, > CIBBIM-Nanomedicine, > Vall d'Hebron Hospital Research Institute, > Passeig Vall d'Hebron 119-129, > Barcelona 08035, Spain. > Tel: +34-93-489-4056 > > Fax: +34-93-489-3893 > Email: sarah.bazzo...@vhir.org > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
