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Michael Barnes
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80
@michael-barnes-354
Last seen 10.2 years ago
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.