[BioC] Post-justRMA "quality control"

[James MacDonald]

The hist and boxplot functions you are trying to use are intended for
AffyBatch objects, not exprSet objects, which is what you have after
running RMA.

Also, I don't think you will be able to simply normalize an AffyBatch
if you use the default quantile normalization. I reported a bug in
normalize.AffyBatch.quantiles about two months ago, where I couldn't
normalize 9 U-133A chips with 2 Gb RAM. To my knowledge this has not
been fixed. You might try normalize(abatch, method="invariantset") or
one of the other normalization procedures.

HTH,

Jim


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Michael Barnes" <Michael.Barnes at cchmc.org> 08/20/03 11:23AM >>>
I am trying to follow the "Load Data" Vignette in the section entitled
"quality control through data exploration".  I am using R1.7.1 and
updated Bioconductor Tuesday (yesterday) on a Windows XP machine.  I
have 23 U133A chips that I am trying to examine.

As I followed the process I was able to do all the actions (histogram,
boxplot, RNA degradation plot) on my dataset. 
> data<-ReadAffy()

> data
AffyBatch object
size of arrays=712x712 features (91097 kb)
cdf=HG-U133A (22283 affyids)
number of samples=23
number of genes=22283
annotation=hgu133a
>

I then wanted to see what my data looked like following normalization
(similar to what is described from pg 23 on).  However, due to memeory
issues I could not run the example in a manner similar to that
described

> normalized.data<-normalize(data[1:23])
Error: cannot allocate vector of size 91091 Kb

 so  I ran justRMA

> normalized.data<-justRMA()
Background correcting
Normalizing
Calculating Expression

> sampleNames(normalized.data)
 [1] "1082_U133A.CEL"       "1083_HG_U133A.CEL"    "1085_U133A.CEL"   

 
 [4] "1087_U133A.CEL"       "109335_U133A.CEL"     "109338_U133A.CEL" 

 
 [7] "109341_U133A.CEL"     "109404_HG_U133A.CEL"  "1095_U133A.CEL"   

 
[10] "110256_U133A.CEL"     "110259_U133A.CEL"    
"110442_HG_U133A.CEL" 
[13] "110443_HG_U133A.CEL"  "110444_HG_U133A.CEL" 
"110445_HG_U133A.CEL" 
[16] "1349_U133A.CEL"       "1460_U133A.CEL"      
"7021.31_HG_U133A.CEL"
[19] "7113.3_HG_U133A.CEL"  "7118.3_HG_U133A.CEL" 
"7149.3_HG_U133A.CEL" 
[22] "813.31_HG_U133A.CEL"  "F1089_U133A.CEL"     

> normalized.data
Expression Set (exprSet) with 
        22283 genes
        23 samples
                 phenoData object with 1 variables and 23 cases
         varLabels
                sample: arbitrary numbering
>

Now I can not get boxplot or histogram.  I have not tried RNA
degradation plot.

> boxplot(normalized.data,col=c(2,2,3,3))
Error in boxplot.default(normalized.data, col = c(2, 2, 3, 3)) : 
        invalid first argument
>

> hist(normalized.data[1:2])
Error in hist.default(normalized.data[1:2]) : 
        `x' must be numeric
>

If Ihave created an incompatible objecct with justRMA, how do I create
the correct object type?  If not, what suggestions do you have.

Michael Barnes, Ph.D.

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