[BioC] Trouble with gcrma background correction

[Sucheta Tripathy]

Hi Herve, Group,

Thanks for your response. As suggested by you, I have installed R version
2.4.0 with bioconductor 1.9. I recreated the cdf environment and computed
affinity data.

I still get the same error:
============================
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames,
  :
    invalid type (NULL) for variable 'affinities'
Execution halted

Following is my sessionInfo():
==============================
R version 2.4.0 (2006-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=en_US;LC_MESS
AGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=e
n_US;LC_IDENTIFICATION=C

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

And the error comes from this code fragment. Possibly I am passing wrong
arguement for type fullmodel.

Code sample:
============

for(i in 1:ncol(pms)){
 if(verbose) cat(".") if(type=="fullmodel"){
  cat("type is fullmodel\n")  # ERROR HERE

    pms[,i] <- bg.adjust.fullmodel(pms[,i],mms[,i],
                                  pm.affinities,mm.affinities,
                                  index.affinities,k=k, rho=rho,fast=fast)

    cat("bg.adjust.fullmodel is done\n")

 pms[index.affinities,i] <- 2^(log2(pms[index.affinities,i])-
 fit1$coef[2]*pm.affinities+mean(fit1$coef[2] *pm.affinities))

 }

====

Any help in solving this will be greatly appreciated.

many thanks

Sucheta


On Fri, November 17, 2006 1:21 pm, Herve Pages wrote:
> Hi Sucheta,
>
>
> Sucheta Tripathy wrote:
>
>> Dear Group,
>>
>>
>> (Sorry for the repost- The earlier one could not get through)
>> I am stuck with this problem for quite some time. I have been searching
>> for an answer to this, but could not quite get a hold of it. Any help in
>>  this will be greatly appreciated.
>>
>> I am using R version 2.3.1 and bioconductor version 1.9.
>>
>
> We strongly discourage you of doing this. Bioconductor 1.9 has been
> designed and tested for R 2.4.z. It is not supported for R 2.3.z users so
> you are on your own...
>
>>
>> First I computed affinity using the following command:
>>
>>
>> affinity.info <- compute.affinities("Soybean", verbose=TRUE)
>> save(affinity.info,file = "soybean.RData");
>>
>> Then I load it using:
>>
>>
>> library(gcrma) load("soybean.RData") source("gcrmaBG.R")
>>
>> when I run the script gcrmaBG.R inside another script, I get the
>> following error:
>>
>>
>> ERROR MESSAGES:
>> ===============
>> Adjusting for optical effect.Done.
>> In first if and type is
>> Adjusting for non-specific binding
>> .type is fullmodel
>> Error in model.frame(formula, rownames, variables, varnames, extras,
>> extranames, :
>> invalid variable type for 'affinities' Execution halted
>>
>
>
> I suggest you upgrade to R 2.4.0 first and see if you can reproduce this
> error. Also, don't forget to provide the output of sessionInfo() so, among
>  other things, people know with version of gcrma you are using.
>
> One last advice: the long script you provided below doesn't help much
> because:
>
>
> (1) some lines have been cut in the middle of a variable name
> if(type=="mm") pms[,i] <-
> bg.adjust.mm(pms[,i],correction*mms[,i],k=k,fast=f ast) so we can't just
> copy and paste it into a file and expect it to work without some extra
> editing work
>
> (2) it's too long
>
>
> Please try to reproduce the error in a few lines of code (no more than
> 10)
> and send only those 10 lines (with sessionInfo output).
>
> Thanks,
>
>
> H.
>
>
>
>>


-- 
Sucheta Tripathy, Ph.D.
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606

web page: http://staff.vbi.vt.edu/sutripa
blog    : http://genomics-array.blogspot.com/