## User: Marcus Davy

Marcus Davy680
Reputation:
680
Status:
Trusted
Location:
Last seen:
10 years, 6 months ago
Joined:
16 years ago
Email:
m****@hortresearch.co.nz

#### Posts by Marcus Davy

<prev • 68 results • page 3 of 7 • next >
2
455
views
2
... Hi, member[2] - member[3] is going to give an error os the binary operator "-" cannot operate on strings, > member[2] - member[3] Error in member[2] - member[3] : non-numeric argument to binary operator try, design <- diag(3)[rep(1:3, each=2),] colnames(design) <- member member <- LE ...
written 13.0 years ago by Marcus Davy680
1
395
views
1
Answer: A: Dist of exprSet object
... P 17 of the vignette("affy"). e.g. chipCols <- rainbow(ncol(exprs(affybatch.example))) boxplot(affybatch.example, col=chipCols) Marcus On 7/27/06 10:40 AM, "Marco Blanchette" wrote: > Thank you all, > > Using bioclite to download the annotation fixed the problem. > > Now, I ...
written 13.0 years ago by Marcus Davy680
1
628
views
1
... Yes the spot intensities (labeled "Empty") which are recorded in a GenePix gpr file should be distributed similarly to the background intensities on a 16 bit GenePix scanner (between 0 and several hundred). Essentially they are measures of background in the foreground spot area. Yes I mean A value ...
written 13.0 years ago by Marcus Davy680
1
628
views
1
... Just to add further comment to this discussion about empty spots in GenePix. Empty spots could be due to the physical printing not taking place at that spot position or buffer which contains no physical cDNA/oligo probe could be deposited by the printing quill at that spot position. In gpr files ...
written 13.0 years ago by Marcus Davy680
2
413
views
2
... Hi, Default function arguements in limma use background subtraction of information (Section 6.1 p20, 20-Apr-2006 edition). I guess more clarity could go into the help pages for plotMA and plotMa3by2 themselves ( This applies to plotPrintTipLoess aswell). A simple way to change the behaviour is to ...
written 13.2 years ago by Marcus Davy680
2
560
views
2
... Jenny, help(readTargets) mentions that If 'row.names' is null, then the column 'Labels' will be used if such exists or, failing that, the column 'FileName'. This looks like a small typo as the column has to be "Label" not "Labels" in ReadTargets <- function(){ ... if ("Label" %in% names( ...
written 13.6 years ago by Marcus Davy680
3
1.3k
views
3
... The colorspace dependency is available from any cran mirror, e.g. http://cran.au.r-project.org/src/contrib/Descriptions/colorspace.html Marcus On 10/20/05 7:58 AM, "Naomi Altman" wrote: > I just downloaded R 2.2.0 for Windows, after which I installed > several Bioconductor packages using ...
written 13.8 years ago by Marcus Davy680
1
304
views
1
... Hi, Doe this include modifying normalizeMedianDeviations aswell for consistency. I suspect normalizeMedianDeviations doesn't reach R's limit as quickly. Marcus MA <- new("RGList") n <- 200 genes <- 1000 MA$M <- matrix(runif(n*genes, -8, 8), nr=genes, nc=n) MA$A <- matrix(run ...
written 13.8 years ago by Marcus Davy680
1
378
views
1
... Hi, I am getting the exact same problem on a fresh install of OS X 10.4 on a G5 patched to 10.4.2 . On starting the R.app, and starting X11, and running the commands; library(affy) ReadAffy(widget=T) I hear the CPU fans kick in and the R.app and tcltk window becomes non responsive. This also hap ...
written 13.9 years ago by Marcus Davy680
1
345
views
1
... you can use the function RG.MA to convert your M and A values back into normalized R and G values. > RG.MA function (object) { object$R <- 2^(object$A + object$M/2) object$G <- 2^(object$A - object$M/2) object$M <- NULL object$A <- NULL new("RGList", unclass(obje ...
written 14.0 years ago by Marcus Davy680 • updated 14.0 years ago by Jianping Jin890

#### Latest awards to Marcus Davy

No awards yet. Soon to come :-)

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.