Hi,
 I am very new to biocondunctor and microaray. I have limited experience
with R.
I am trying to use biocondunctor for analyzing HuGene-1_0-st-v1 microarray
data. I selectected different normalization method (rma, gcrma and mas5).
For my data rma worked but for for gcrma and mas5 both I have problem.
For gcrma it gives me a error like: Computing affinitiesError:
length(prlen) == 1 is not TRUE

And for mas 5 it seems working but I get only a whole list of NA.

Here is what I have done.

> mydata <- ReadAffy()
> mydata
AffyBatch object
size of arrays=1050x1050 features (16 kb)
cdf=HuGene-1_0-st-v1 (32321 affyids)
number of samples=18
number of genes=32321
annotation=hugene10stv1

> eset <- rma(mydata)
Background correcting
Normalizing
Calculating Expression
> eset_justrma=justRMA()
> eset_mas5 <- mas5(mydata)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
32321 ids to be processed
|                    |
|####################|
> eset_gcrma <- gcrma(mydata)
Adjusting for optical effect..................Done.
Computing affinitiesError: length(prlen) == 1 is not TRUE   Here is the
error

> eset_justrma # this worked fine
ExpressionSet (storageMode: lockedEnvironment)
assayData: 32321 features, 18 samples
  element names: exprs, se.exprs
protocolData
  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL ...
MC9_(HuGene-1_0-st-v1).CEL (18 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL ...
MC9_(HuGene-1_0-st-v1).CEL (18 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hugene10stv1
> eset_mas5 # this seems worked fine but resulted all NA
ExpressionSet (storageMode: lockedEnvironment)
assayData: 32321 features, 18 samples
  element names: exprs, se.exprs
protocolData
  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL ...
MC9_(HuGene-1_0-st-v1).CEL (18 total)
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: MC1_(HuGene-1_0-st-v1).CEL MC10_(HuGene-1_0-st-v1).CEL ...
MC9_(HuGene-1_0-st-v1).CEL (18 total)
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hugene10stv1
> write.exprs(eset_justrma,file="eset_justrma.csv")
> write.exprs(eset_mas5,file="eset_mas5.csv")
> write.exprs(eset,file="eset.csv")

Any help in this will be really great. Being a novice, I am very sorry if I
am doing any silly mistake.
Thanks a lot,
Suparna.

-- 
Dr. Suparna Mitra
Wolfson Centre for Personalised Medicine
Department of Molecular and Clinical Pharmacology
Institute of Translational Medicine University of Liverpool
Block A: Waterhouse Buildings,  L69 3GL Liverpool

Tel.  +44 (0)151 795 5414, Internal ext: 55414
M: +44 (0) 7523228621
Email id: smitra@liverpool.ac.uk
Alternative Email id: suparna.mitra.sm@gmail.com

	[[alternative HTML version deleted]]

