similar to: how to remove NA/NaN/Inf in a matrix??

Displaying 20 results from an estimated 300 matches similar to: "how to remove NA/NaN/Inf in a matrix??"

2005 Nov 10
1
Help regarding mas5 normalization
Hello everybody, I am trying to use mas5 to normalize some array data and using mas5 and mas5calls. But I received these warning message. If anybody can explain the problem I would really appreciate that. Thanks in advance. background correction: mas PM/MM correction : mas expression values: mas background correcting...Warning message: 'loadURL' is deprecated. Use 'load(url())'
2011 Sep 14
1
how to get a row with its its p value below 0.01 ??
Hi all, I'm analyzing micro array data.. it has produced a file (to be specific matrix) withdimension of 35556 2. first few lines of the matrix are as below.. probe_name control.fdr.pvals.present 10338001 0.000440001 10338002 0.000583093 10338003 0.000528449 10338004 0.000610362 10338005 0.000151825 10338006 0.0001733 10338007 0.000152924 Now, i want only rows whose
2006 Jul 25
0
Normalization problem
At first I would like to express the gratitude toward Oosting, J. and James MacDonal for their help solving the previous problem I posted on this forum. Now I have a new problem. I was trying to normalize set of microarray data on HGU133 paltform. I put all the HGU133A platform chips in one directory and all the other HGU133B chips on another directory. When I tried to normalized them using same
2011 Nov 18
1
how to normalize a subset of affy data using MAS5 method
Dear all, I was trying to normalize a subset of affy data those transcribe are either P or M (called pm_filter). I am able to normalize pm_filter subset by using RMA method, however MAS5 is not working. For RMA method, I used the following commend: est<-rma(affydata, subset=pm_filter). Could any help me; how do I do this by using MAS5 method? Regards, Anup Som -- Dr. Anup Som,
2010 Aug 04
1
error with ReadAffy()
Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >
2004 Aug 19
1
A question about memory size
Hi.... I have a question about how to increase my memory size, could someone answer it for me?? I am using Bioconductor in R to calculate gene expression values with mas5, dchip, and mas4. I have only 18 samples, all from Affymetrix U133A Plus 2 arrays, which has ~54,000 genes. My machine equipments are: CPU P4 3.0GHz, and 1GM RAM. Somehow when I was running mas5 in R, it always showed the error
2005 Aug 31
1
Bioconductor and R-devel
Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,
2006 Nov 11
1
Install bioconductor
Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message
2003 Jan 23
1
order() on vector with Inf's
I have a parameter vector, ibeta, and a corresponding vector of loglikelihoods, llbet. If llbet contains no NAs or Inf's then I can extract the best parameter by index <- order(-llbet)[1] beta <- ibeta[index] or similar. The argument na.last of order() allows me to fix this up even if llbet contains some NAs which I wish to ignore. Unfortunately my llbet contains Inf's, which
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2003 Oct 30
0
Release of Bioconductor 1.3
The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?
2020 May 29
2
LLVM Support needed
I wanted confirm answer from you guys. Request you to provide authentic information on this. Best Regards / Mit freundlichen Grüßen Minal Kulkarni Knorr Bremse Technology Center India Survey No.276, Village Mann, Hinjewadi, Phase II, Tal.Mulshi, Pune - 411 057. Maharashtra , India. Phone: +91 9028098122 Mobile: mailto:minal.kulkarni at knorr-bremse.com
2020 May 28
2
LLVM Support needed
Hello Dear Team, I wanted to know in which version of LLVM Tricore architecture is supported. I have LLVM 2.8 with me which has no support for Tricore. Basically I wanted to add Aurix target support. Could you please help me. Best Regards / Mit freundlichen Grüßen Minal Kulkarni Knorr Bremse Technology Center India Survey No.276, Village Mann, Hinjewadi, Phase II, Tal.Mulshi, Pune - 411
2008 Jul 24
4
Dividing by 0
I'm trying to calculate the percent change for a time-series variable. Basically the first several observations often look like this, x <- c(100, 0, 0, 150, 130, 0, 0, 200, 0) and then later in the life of the variable they're are generally no more 0's. So when I try to calculate the percent change from one observation to the next, I end up with a lot of NA/Nan/INF, and
2016 Apr 05
0
Re: [PATCH 1/7] v2v: check next free oem%d.inf in /Windows/Inf
On Tue, 2016-04-05 at 15:13 +0300, Roman Kagan wrote: > On Tue, Apr 05, 2016 at 01:47:27PM +0200, Cédric Bosdonnat wrote: > > It seems that checking for oem%d.inf in the DeviceIds registry > > entry > > doesn't always list all oemXX.inf files. For example we may have > > oem1.inf free in the registry key, but used in another one. > > In my experiments this
2005 Apr 13
2
Inf +1i vs 1+Inf*1i
Hi If I have a <- Inf + 1i then Re(a) is Inf, and Im(a) is 1, as expected. But if b <- 1 + Inf * 1i, then Im(b) = Inf , as expected, but Re(b) = NaN, which I didn't expect. Why this asymmetry? How to define an object with Re(b)=1, Im(b)=Inf? -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre European Way, Southampton SO14 3ZH, UK tel 023-8059-7743
2007 Jun 13
2
Removing Inf and Inf values from a fata frame
Hi, I have a csv file with empty values, when I apply the different functions (mean, std, etc.) I create a new data frame, the empty values generate Inf and -Inf values. How can I remove those Inf and -Inf values from the new data frame? I already specified na.rm in the mean and std functions, but the values are still there. Thank you, Judith
2012 May 04
2
Test if a sample mean of integers with range -inf; inf is different from zero
Hi all, how would you test if a sample mean of integers with range -inf;inf is different from zero: # my sample of integers: c <- c(-3, -1, 0, 1, 0, 3, 4, 10, 12) # is mean of c <> 0?: mean(c) Thanks, Kay [[alternative HTML version deleted]]
2002 Jan 25
0
max/min of NULL gives MININT/MAXINT instead of -INF/+INF (PR#1283)
R Version 1.4.0 Patched (2002-01-23) Solaris 5.8 I just noticed that max(NULL) gives a strange result: > max(NULL) [1] -2147483647 Warning message: no finite arguments to min/max; returning extreme. in: max(..., na.rm = na.rm) I discovered this when I did something like max(object$element) for an incorrect element name. The warning message was helpful, but I was still surprised to
2016 Apr 05
0
Re: [PATCH 1/7] v2v: check next free oem%d.inf in /Windows/Inf
On Tue, 2016-04-05 at 13:04 +0100, Richard W.M. Jones wrote: > On Tue, Apr 05, 2016 at 01:47:27PM +0200, Cédric Bosdonnat wrote: > > + let oem_inf = set_free_oem_inf g root scsi_adapter_guid > > "viostor.inf" driverdir in > > Seems better if it was called *get_next*_free_oem_inf? Yes, sounds better. > > (* There should be a key > > *