search for: mrna

...nded DNA specific 5'-3' exodeoxyribonuclease activity 09127-GOTERM 'de novo' actin filament nucleation 09180-GOTERM 5'-tyrosyl-DNA phosphodiesterase activity 09282-GOTERM deoxyribonucleoside 5'-monophosphate N-glycosidase activity 09330-GOTERM 3'-UTR-mediated mRNA stabilization 09355-GOTERM histone pre-mRNA 3'end processing complex which has two tab-delimited columns. I used read.table("",as.is=TRUE) and ended up with fewer lines so I have to use quote="" which also works if any line contains only a singe double (") quote....

...sing scripts. 1. Description of the data 1.1. there are 5 text files, each of which contains cleaned data for the same 100 SNPs. Observations (e.g., position on gnome, alelle type, ...) for SNPs are rows ordered by the SNP numbers, 1.2. there are 1 text file, containing the expression level of mRNAs 9 (and other information), which are rows ordered by mRNA numbers, So for each SNP the sample size is 5. 2. Description of aim Take SNP 1 and mRNA 1 for example. Write a scrip that can 2.1 extract row 1 from each of the 5 text files for SNP data 2.2 extract row 1 from the mRNA text file 2.3...

Hi there, I wonder if there is a way of efficiently generating a correlation matrix of two expression matrices. I want to correlate miRNA and mRNA expression and used the following code: ##dat.mi miRNA expression matrix, dat.m mRNA expression matrix nc <- nrow(dat.mi) cor.mat <- data.frame(rep(NA,nrow(dat.m))) pval.mat <- data.frame(rep(NA,nrow(dat.m))) for(i in 1:nc) { cr <- vector() pv <- vector() print(paste(i," mirs ou...

...frames with different number of observations but the same number of variables (columns) An example, if I write str(object1), I see this, data.frame': 47 obs. of 3 variables: $ ORF : Factor w/ 245 levels "YAL038W","YAL054C",..: 10 19 38 39 44 45 50 51 59 60 ... $ mRNA : num 0.891 1.148 1.202 1.479 1.445 ... $ Protein: num 1.230 1.288 1.175 0.724 0.851 .. str(object2) 'data.frame': 21 obs. of 3 variables: $ ORF : Factor w/ 245 levels "YAL038W","YAL054C",..: 11 25 40 55 66 78 104 119 141 153 ... $ mRNA : num 0.794 0.74...

...") to calculate correlation between all possible pairs. But the issue is that there is one-many specific mappings between A and B and I just need to calculate correlations for those pairs (not all). Some variables in A (proteins, say p1) have more than 3 (or 2 or 1) corresponding mapping in B (mRNA, say, m1,m2,m3) and I would like calculate correlations between p1-m1, p1-m2, and p1-m3 and then for the second variable p2 etc.  I have the mapping information in another file (annotation file). Could you please suggest me how to do that? Thanks in advance. Kind regards,Ezhil   [[alternative HTML...

Hello, I have a seemingly simple problem that a tab-delimited file can't be read in. > annoTranscripts <- read.table("matched.txt", sep = '\t', stringsAsFactors = FALSE) Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 5933 did not have 12 elements However, all lines do have 12 columns. > lines <-

...inbind... I get this: winbind -i -d100 winbindd version 2.2.6 started. Copyright The Samba Team 2000-2001 Initialising global parameters params.c:pm_process() - Processing configuration file "/usr/local/etc/smb.conf" Processing section "[global]" doing parameter netbios name = mRNA handle_netbios_name: set global_myname to: MRNA doing parameter workgroup = chemputers doing parameter server string = mRNA Samba server - It's unix baby! doing parameter wins support = No doing parameter wins server = 192.168.100.253 192.168.100.252 wins_srv_load_list(): Building WINS server l...

...expect to read much more. Terry Therneau -------- begin included message --------- I want to test the expression of a subset of genes for correlation with patient survival. I found out that the coxph function is appropriate for doing this since it works with continuous variables such as Affy mRNA expression values. I applied the following code: cp <- coxph(Surv(t.rfs, !e.rfs) ~ ex, pData(eset.n0)) #t.rfs: time to relapse, status (0=alive,1=dead), ex: expression value (continuous) The results I get look sensible but I would appreciate any advice on the correctness and also any sugge...

...#39;-3' exodeoxyribonuclease activity > 09127-GOTERM 'de novo' actin filament nucleation > 09180-GOTERM 5'-tyrosyl-DNA phosphodiesterase activity > 09282-GOTERM deoxyribonucleoside 5'-monophosphate N-glycosidase activity > 09330-GOTERM 3'-UTR-mediated mRNA stabilization > 09355-GOTERM histone pre-mRNA 3'end processing complex > > > which has two tab-delimited columns. I used read.table("",as.is=TRUE) and ended up with fewer lines so I have to use quote="" which also works if any line contains only a singe dou...

...e up-regulated compared to the universal iis upr-egulated, and >>what is down-regulated looks down-regulated. The difference is that the >>down-regulated (and not in the up), so so much more down-regulated in one >>of the batches. It looks like to be that the universal has more mRNA >>abundance in one batch over the other. > >Gquantile won't help because it doesn't change the M-values. (It is >intended for use with single channel analyses.) You could try 'quantile' >or 'scale' normalization (not both) but there are no magic bullets...

...frame(a2,a3) tarmat[a2,i] = a3 } What is the problem then: The problem is a2 has ' (single quotes). So when a2 does not have singles quote, everything works fine. But when a2 has ' - then starting from there to the EOF all values are cluttered. Example: > a2[49] [1] "mRNA guanylyltransferase activity" > a2[50] [1] "polynucleotide 5-phosphatase activity\t1\t1\t0.0160650535501781\t0.0160650535501781\t0.0664390950962566\nribulose-phosphate 3-epimerase activity\t1\t1\t0.0160650535501781\t0.0160650535501781\t0.0664390950962566\n How can I escape the '...

Hi ! I would like to understand where do affinity.spline.coefs used in function compute.affinities come from ? library(gcrma) data(affinity.spline.coefs) affinity.spline.coefs X1 X2 X3 X4 X5 X1 -0.55004171 -0.58579091 -0.08870557 -0.47774242 0.23205570 0.58002746 X2 X3 X4 X5 X1 X2

...esponding DSPL (XML) metadata file jointly with the CSV files. All zipped up and ready to be published at Public Data Explorer. * gsmaRt (1.0) Maintainer: Stephan Artmann Author(s): Stephan Artmann, Mathias Fuchs License: GPL http://crantastic.org/packages/gsmaRt combined miRNA- and mRNA-testing * HIest (1.0) Maintainer: Unknown Author(s): Ben Fitzpatrick License: GPL (>= 3) http://crantastic.org/packages/HIest Uses likelihood to estimate ancestry and heterozygosity. Evaluates simple hybrid classifications (parentals, F1, F2, backcrosses). Estimates genomic cline...

I am trying to create a frequency distribution and I am a bit confused. Here are the commands I have entered: > data <- read.csv(file="40609_sortedfinal.csv",head=TRUE,sep=",") > NumberOfActionsByStatus = data$STATUS > NumberOfActionsByUser = data$ETS_LOGIN > NumberOfBidOffer = data$BID_OFFER > NumberOfActionsByUser.freq = table(NumberOfActionsByUser) >