similar to: pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up"))

Hi List I have data in the following form: Gene    TFBS NUDC     PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) HLF(191) RPA2     STAT4(57) HEB(251) TAF12     PAX3(53) YY1(92) BRCA(99) GLI(101) EIF3I     NERF(10) P300(10) TRAPPC3     HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122) TRAPPC3     EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121)

I'm putting together an R package. I would like to show example code in the vignette, where example data files (included in the package) are used to generate an (example) output file. I read about using example data in Hadley Wickham's post ( http://r-pkgs.had.co.nz/data.html), and believe I should keep my example data as raw data, as it must be parsed to generate the output. So, I

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HTML version deleted]]

Hi, I have the following newbie question, it is possible have two (or more) domains in the same IP subnetwork (e.g. 192.168.10.0/24)? I understand that is not possible have two PDC for the same domain in the same subnetwork, but I'm not sure what happens if we have two domains. Thanks for your help. Regards, -- Mauricio Strello C.

Hi, I plan to reorganise our IP management and I'd like to implement a slave DHCP server. Right now we assign IP addresses based on the ethernetadress of a client 1:1. The tutorial here [1] is simple and looks like the thing I need. I do have a lot of subnetworks and my cisco router has an DHCP helper address set. I know I'll have to add the second dhcp-server address. My questions now

I am trying to create a pie chart using rpy2 of the following data Pathway Occurrences A 10% B 50% C 20% E 10% filename = './testing.png' grdevices = importr('grDevices') rdevices.png(file=filename, width=1200, height=800) dataf = Robjects.DataFrame({'pathways':Robjects.StrVector(Pathways),

I feel I should know the answer to this, but I wanted to verify. I have a bunch of Windows PC's running Win 2K Pro, on three subnetworks. Two of the subnets are served by Unix (FreeBSD) boxes running NATD, but all are joined to a domain being run on a Win 2K Pro server in another building on the campus. So far I haven't joined the two Unix boxes to the domain. I'd like to

Hello, Does anyone know of a way of finding all the nodes that are between a pair of specified nodes in the excellent graph package (R vers 2.5.0). I have a class(graphAM) object and need to determine all possible pathways in this object. Here's an example: In the simple case of a--b--c (where -- denotes "conected to") the list of all pathways would be: ab ba abc cba cb bc.

Greetings all, I have two sets of data that I would like to investigate. The first is gene/genome related data given different 'cell-states'. The second set of data is relates the genes to a biological pathway. /(I think in pictures so here goes.)/ *dataframe1* gene, cell-state1, cell-state2 gene1, x1, y1 gene2, x2, y2 gene.x, ..., ... *dataframe2* pathway1, gene-x1, gene-x2, ...

Hi there, I am trying to run an MCMC on stable isotope data from certain organisms to determine their dietary habits in the package SIAR. I have prepared my data according to Inger, R., Jackson, A., Parnell, A., Bearhop, S. : SIAR V4 (Stable Isotope Analysis in R) an Ecologist's Guide (also better known as 'SIAR for dummies'), which is as follows: - consumer data table (columns

For some reason when I apply a function to a single row in R it works, but when that same row is in a data.frame it does not, see below: apply(dx[954,], 1, query.db) 2571 1092 0.06044147 3890 0.05948577 3273 0.05911261 794 0.05855583 4241 0.05854064 3560 0.05602690 apply(dx[954:955,], 1, query.db) $`2571` numeric(0) $`1194` 908 3754 5119 2835

Hi thanks Roger, I've amended my hosts.allow file to your suggested one - thanks for that. I'm still getting "Connection refused on the client cgi screen as well as in the shell it gives me UPS upsname at ipaddresshere is unavailable... Any ideas what I can try next to debug why it's not working. Also should the "allowfrom = clientIPaddresshere" line be in my monuser

I'm having problems with this example, it is posted with reproduceable code below, both with the normal 0-6 scale and the desired 3-6 scale (with bars removed). How can I get the graph to have the desired 3-6 scale without removing the bars. Thanks! #Data

Hi, is it possible, to configure one physical samba server to listen on multiple NICs? I have two subnetworks to which I'd like to connect my samba server, but I dont want both networks to "see" each other, so the server should not be a router. The Clients in both networks should see the same serverstructure (Users, Shares,...) Thanks for any hints and tips! cu... ...G?tz --

Hello all, Name is Andrew and in desperate need of some info. Setup: - Mandrake 9.1 with three interfaces (eth0 --> WAN) C-class /28 network (with tree virtual addresses which I am DNAT-ing to the DMZ) (eth1 --> LAN) A-class 10.0.0.0/8 (eth2 --> DMZ) A-class subnet 10.1.123.0/24 - Running stock Shorewall ver: shorewall-1.3.14-3.1.91mdk Dilemma: - LAN can not access the DMZ zone

Dear all, we seek a talented and motivated post-doc to develop computational methods for inferring the molecular basis of genetic diseases by integration of personal omics data. Research topics include: identifying causal mutations of rare disease patients by meta-analysis; inferring disease-causing molecular pathways from genotype, phenotypes, and omics profile of patient-derived cell lines

Hi, we do have some subnetworks for private computers, which are allowed to use there public smtp servers like msn, web.de or whatever with the users private accounts. All our own computers have to send mail trough our mailserver with user authentication. From time to time we are faced with the fact, that a virus infected private notebook sends spam and we are told by our ISP to take care :)

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs..

Hi * I have a question about windows network browsing from linux box in a multi-subneted network. I have such network topology: my subnet is 10.105.27.224/27, there are 10 boxes in my subnet; also there are several other subnets - 10.105.27.0/27, 10.105.27.96/27, ..., 172.17.51.64/27, ..., 172.17.48.0/26, ... In our network we have one wins server with ip 172.17.48.13 that very likely configured