[BioC] Does old workspace work?

Loren Engrav engrav at u.washington.edu
Mon Nov 10 20:50:05 CET 2008


So I fixed up the old workspace from early 2007 with all your help
Installed 64bit Intel MacOS stuff
Installed the new BioC maanova stuff
Changed one of the 60 chips
And reran the mixed linear regression previously done in early 2007
The command was

ftest.Breed.mix_1000perm081109 <- matest
(BDeset_gcrma_NoCon25LRmadata.raw.WithAffyID081109, BGanova.Br_T.mix081109,
term = ³Breed², n.perm = 1000, critical = .9, test.type = c("ftest"),
shuffle.method = c("sample"), MME.method = c("REML"), test.method =
c(1,0,1,1), pval.pool = TRUE, verbose = TRUE)

In early 2007 this process took about 40 hours
This time it took 15 hours which is a serious improvement

Four derivative questions Please
#1I noticed the computer was using only one of the 8 processors
Can R/BioC use all of the processors?

I received this warning many many times
50: In any(parsed.formula$random) ... : coercing argument of type 'double'
to logical
#2Is this significant?

I have 64bit R.app but to install the 64bit packages I quit R.app and in
terminal do
source ("http://www.bioconductor.org/biocLite.R")
biocLite (c("whatever"), type="source")
It seems I cannot install the 64bit packages from R.app
#3Is this true? This has been discussed but I cannot find the definitive
skinny

In the old workspace there are several objects like
"biocinstall.defaultPkgs"
"biocinstall.graphPkgs"
"biocinstall.litePkgs"
 which are scripts of various types I guess to install groups of packages,
like

function()
{
        contriburl = "http://bioconductor.org/packages/1.9/bioc/src/contrib"
        available.packages(contriburl)[, "Package"]
}

#4Are these scripts old and no longer used to install groups?

Thank you again

> From: Loren Engrav <engrav at u.washington.edu>
> Date: Fri, 31 Oct 2008 15:38:12 -0700
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Does old workspace work?
> 
> Cool, I can deal with evolution
> 
> And the archives will be a super addition to ? and google, thank you, maybe
> better than google
> 
> So we biopsied shallow and deep wounds on 3 Duroc pigs and 3 Yorkshire pigs
> at 1 2 3 12 and 20 weeks, this then is 60 porcine chips with 24123 probe
> sets on the chip, we were interested in chip2-chip1, chip4-chip3, etc
> And studied the differences with R/maanova and various biologic data
> reduction steps to achieve a group of 1289 for further study
> 
> So for the fun of it,  I compared chip2-chip1 in gcrmaOld and gcrmaNew
> 
> In gcrmaOld there were no differences of exactly zero
> In gcrmaNew 249/24123 were exactly zero which seems kinda funny
> This affected 4 in the group of 1289 but did not change anything
> 
> 9247/24123 differences changed sign which is potentially bad for this study;
> but after cutting those with log ratio < .5 as too trivial to worry about in
> this complex system, zero were left
> 
> I could rerun this, but given this, and that the old Mac PRO PPC took ~40
> hours to run the mixed linear regression, I think the old data is just fine
> 
> And since 
> objNew <- as(objOld, "ExpressionSet") works would appear I am back in
> business
> 
> Thank you all
> 
> 
> From: Sean Davis <sdavis2 at mail.nih.gov>
> Date: Fri, 31 Oct 2008 15:00:47 -0400
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Does old workspace work?
> 
> 
> 
> On Fri, Oct 31, 2008 at 2:47 PM, Loren Engrav <engrav at u.washington.edu>
> wrote:
>> Thank you, got it
>> 
>>  exprs(obj) is missing from the output but shows in ?ExpressionSet and puts
>> up the data so I can see it
>> 
>> And now perhaps one final question to understanding this old data and
>> progress
>> 
>> Long long ago I did
>> AA_ReadAffy <- ReadAffy()
>> ABeset_gcrma < gcrma (AA_ReadAffy)
>> 
>> Now I do
>> AA_ReadAffy081031 <- ReadAffy() #on the same .cel files
>> ABeset_gcrma081031 <- gcrma (AA_ReadAffy081031)
>> 
>> Then I do
>> Show(ABeset_gcrma) and exprs(ABeset_gcrma081031)
>> 
>> And they do not match, for example
>> Probe set Ssc.10026.1.A1_at
>> ABeset_gcrma is 4.124689
>> ABeset_gcrma081031 is 3.344443
>> 
>>  ReadAffy changed?
>>  gcrma changed?
> 
> See:
> 
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/16664/fo
> cus=16664
> 
> The bioconductor archive is your friend.
> 
> Sean
> 
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