[BioC] Post-justRMA "quality control"
jmacdon at med.umich.edu
Wed Aug 20 12:58:58 MEST 2003
The hist and boxplot functions you are trying to use are intended for
AffyBatch objects, not exprSet objects, which is what you have after
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.
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
>>> "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.
size of arrays=712x712 features (91097 kb)
cdf=HG-U133A (22283 affyids)
number of samples=23
number of genes=22283
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
Error: cannot allocate vector of size 91091 Kb
so I ran justRMA
 "1082_U133A.CEL" "1083_HG_U133A.CEL" "1085_U133A.CEL"
 "1087_U133A.CEL" "109335_U133A.CEL" "109338_U133A.CEL"
 "109341_U133A.CEL" "109404_HG_U133A.CEL" "1095_U133A.CEL"
 "110256_U133A.CEL" "110259_U133A.CEL"
 "110443_HG_U133A.CEL" "110444_HG_U133A.CEL"
 "1349_U133A.CEL" "1460_U133A.CEL"
 "7113.3_HG_U133A.CEL" "7118.3_HG_U133A.CEL"
 "813.31_HG_U133A.CEL" "F1089_U133A.CEL"
Expression Set (exprSet) with
phenoData object with 1 variables and 23 cases
sample: arbitrary numbering
Now I can not get boxplot or histogram. I have not tried RNA
Error in boxplot.default(normalized.data, col = c(2, 2, 3, 3)) :
invalid first argument
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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