search for: pcc

...e following two that I had a look I am getting different t-values. Does anyone have any clues on why is that? The source code is below. Thanks. pcor3 <- function (x, test = T, p = 0.05) { nvar <- ncol(x) ndata <- nrow(x) conc <- solve(cor(x)) resid.sd <- 1/sqrt(diag(conc)) pcc <- -sweep(sweep(conc, 1, resid.sd, "*"), 2, resid.sd, "*") #colnames(pcc) <- rownames(pcc) <- colnames(x) if (test) { t.df <- ndata - nvar t <- pcc/sqrt((1 - pcc^2)/t.df) print(t); pcc <- list(coefs = pcc, sig = t > qt(1 - (p/2), df = t.d...

Dear All: I have a question on using coxph for multiple genes: I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data. However, I don't know how to work with the result for each gene: survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. 3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox) each time I tried to look at what is in survtest it gives me this: ============================================================================...

...ther software... but if possible someone could have a look and spot any mistakes I would be grateful. Thanks pcor3 <- function (x, test = T, p = 0.05, alternative="two.sided") { nvar <- ncol(x) ndata <- nrow(x) conc <- solve(cor(x)) resid.sd <- 1/sqrt(diag(conc)) pcc <- -sweep(sweep(conc, 1, resid.sd, "*"), 2, resid.sd, "*") #colnames(pcc) <- rownames(pcc) <- colnames(x) if (test) { t.df <- ndata - nvar t <- pcc/sqrt((1 - pcc^2)/t.df) #pcc <- list(coefs = pcc, sig = t > qt(1 - (p/2), df = t.df)); # origin...

...m a data frame which matches to first 2 columns of another data frame. Here is the example what I am trying to do: > ptable=read.table(file="All.txt",header=T,sep="\t") > ptable=as.matrix(ptable) > dim(ptable) [1] 9275 6 > head(ptable) Gene1 Gene2 PCC PCC3 PCC23 PCC123 [1,] "3813_f_at" "3884_f_at" "0.9956842" "0.9955455" "0.9956513" "0.9956171" [2,] "3884_f_at" "3813_f_at" "0.9956842" "0.9955455" "0.9956513" "0....

Hi! All, To find co-expressed genes from a expression matrix of dimension (9275 X 569), I used rcorr function from library(Hmisc) to calculate pearson correlation coefficient (PCC) and their corresponding p-values. From the correlation matrix (9275 X 9275) and pvalue matrix (9275 X 9275) obtained using rcorr function, I wanted to select those pairs whose PCC's are above 0.8 cut-off and then for those gene pairs their corresponding p-values. I did following: library(Hmis...

...erse variance. So compute the variance-covariance matrix, invert, scale to the diagonal and negate and you have it. And an implementation by Martyn Plummer (here, too, I received several): pcor2 <- function(x){ conc <- solve(var(x)) resid.sd <- 1/sqrt(diag(conc)) pcc <- - sweep(sweep(conc, 1, resid.sd, "*"), 2, resid.sd, "*") return(pcc) } This is the version I'm using now, together with a test for significance of each coefficient (H0: coeff=0): f.parcor <- function (x, test = F, p = 0.05) { nvar <- ncol(x) nda...

Dear All: I have a question on using coxph for multiple genes: I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data. However, I don't know how to work with the result for each gene: survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. 3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox) each time I tried to look at what is in survtest it gives me this: ========================================================================...

Hey all, I'm working on adding interprocedural FunctionAttrs optimization ( http://llvm-cs.pcc.me.uk/lib/Transforms/IPO/FunctionAttrs.cpp) to ThinLTO so it does something similar to what LTO is doing ( https://bugs.llvm.org/show_bug.cgi?id=33648). I've hit a problem with how the FunctionAttrs optimization expects linkage types. In ThinLTO since the linkage type is set to External or Ava...

...n failed, deal with it (Note that this is about functions returning bool, not int.) Folks on that review feel that returning true on success is probably what we want, but it's not documented anywhere and we do have both forms in the codebase. True on success seems more common: http://llvm-cs.pcc.me.uk/?q=true+on+success http://llvm-cs.pcc.me.uk/?q=true+on+error Does anyone have a pointer to previous on-list discussion on this? If not, this thread could be the place where we sort this out once and for all :-) Apologies for the bike-sheddy topic. Nico -------------- next part ------------...

On Mon, May 9, 2016 at 4:26 PM, David Blaikie <dblaikie at gmail.com> wrote: > > > On Mon, May 9, 2016 at 3:38 PM, Peter Collingbourne <peter at pcc.me.uk> > wrote: > >> >> >> On Mon, May 9, 2016 at 3:17 PM, Peter Collingbourne <peter at pcc.me.uk> >> wrote: >> >>> >>> >>> On Mon, May 9, 2016 at 2:33 PM, David Blaikie <dblaikie at gmail.com> >>> wrote: >&g...

On Tue, Apr 4, 2017 at 1:25 PM, Mehdi Amini <mehdi.amini at apple.com> wrote: > > On Apr 4, 2017, at 12:12 PM, Peter Collingbourne <peter at pcc.me.uk> wrote: > > On Mon, Apr 3, 2017 at 8:13 PM, Mehdi Amini <mehdi.amini at apple.com> wrote: > >> >> On Apr 3, 2017, at 7:08 PM, Peter Collingbourne <peter at pcc.me.uk> wrote: >> >> Hi, >> >> As part of PR27551 I want to add a string t...

...drivers available: 1) the normal printer driver installed into \\print-srv\print$\x64\3\<lots of DDL, cfg, chm files etc> 2) make reg key PrinterDriverAttributes odd 3) when you now try to deploy a Printer from this print server, Windows will package the driver into \\print-srv\print$\x64\PCC\<your printer>.inf_amd64_neutral_<some random number>.cab 4) client downloads this CAB file and load this driver into the local Driver Store (C:\Windows\System32\DriverStore\FileRepository) 5) printers deploy without problem As a test i copied this packaged driver from 3) into my Sam...

...2016, at 4:42 PM, Peter Collingbourne via llvm-dev < > llvm-dev at lists.llvm.org> wrote: > > > > On Mon, May 9, 2016 at 4:26 PM, David Blaikie <dblaikie at gmail.com> wrote: > >> >> >> On Mon, May 9, 2016 at 3:38 PM, Peter Collingbourne <peter at pcc.me.uk> >> wrote: >> >>> >>> >>> On Mon, May 9, 2016 at 3:17 PM, Peter Collingbourne <peter at pcc.me.uk> >>> wrote: >>> >>>> >>>> >>>> On Mon, May 9, 2016 at 2:33 PM, David Blaikie <dblaikie at...

...config.log ***" Where does the zlib reside on the system? I can't find it anywhere. Thanks. __________________________________________ Benjamin Le Sr. Systems Administrator Information Technology Services Portland Community College Voice:(503)-977-4736 Fax:(503)-977-4987 Mailto:ble at pcc.edu http://www.pcc.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.mindrot.org/pipermail/openssh-unix-dev/attachments/20030408/4f434f73/attachment.html

On Tue, May 10, 2016 at 11:45 AM, David Blaikie <dblaikie at gmail.com> wrote: > > > On Mon, May 9, 2016 at 4:42 PM, Peter Collingbourne <peter at pcc.me.uk> > wrote: > >> >> >> On Mon, May 9, 2016 at 4:26 PM, David Blaikie <dblaikie at gmail.com> wrote: >> >>> >>> >>> On Mon, May 9, 2016 at 3:38 PM, Peter Collingbourne <peter at pcc.me.uk> >>> wrote: >>> &g...

On Mon, Apr 3, 2017 at 8:13 PM, Mehdi Amini <mehdi.amini at apple.com> wrote: > > On Apr 3, 2017, at 7:08 PM, Peter Collingbourne <peter at pcc.me.uk> wrote: > > Hi, > > As part of PR27551 I want to add a string table to the bitcode format to > allow global value and comdat names to be shared with the proposed symbol > table (and, as side effects, allow comdat names to be shared with value > names, make bitcode file...

> On Oct 24, 2016, at 1:07 PM, Peter Collingbourne <peter at pcc.me.uk> wrote: > > On Mon, Oct 10, 2016 at 8:12 PM, Peter Collingbourne <peter at pcc.me.uk <mailto:peter at pcc.me.uk>> wrote: > The specific change I have in mind is to allow !range metadata on GlobalObjects. This would > be similar to existing !range metadata, but it w...

On Mon, May 9, 2016 at 3:17 PM, Peter Collingbourne <peter at pcc.me.uk> wrote: > > > On Mon, May 9, 2016 at 2:33 PM, David Blaikie <dblaikie at gmail.com> wrote: > >> >> >> On Mon, May 9, 2016 at 1:53 PM, Peter Collingbourne <peter at pcc.me.uk> >> wrote: >> >>> >>> >>> On Fri,...

Hi Charles, On Tue, Jul 11, 2017 at 12:27 PM, Davide Italiano <davide at freebsd.org> wrote: >> I'm working on adding interprocedural FunctionAttrs optimization >> (http://llvm-cs.pcc.me.uk/lib/Transforms/IPO/FunctionAttrs.cpp) to ThinLTO >> so it does something similar to what LTO is doing >> (https://bugs.llvm.org/show_bug.cgi?id=33648). I've hit a problem with how >> the FunctionAttrs optimization expects linkage types. >> >> In ThinLTO since...

> On Apr 7, 2016, at 12:39 PM, Peter Collingbourne <peter at pcc.me.uk> wrote: > > > > On Thu, Apr 7, 2016 at 12:29 PM, Mehdi Amini <mehdi.amini at apple.com <mailto:mehdi.amini at apple.com>> wrote: > >> On Apr 7, 2016, at 11:59 AM, Xinliang David Li <davidxl at google.com <mailto:davidxl at google.com>> wrote...