[BioC] Does old workspace work?

[Loren Engrav]

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