[BioC] affycoretools repost

[Louisa A Rispoli/AS/EXP/UTIA]

Hi-

Thank you for your help. I checked that sampleNames(pd) and looks like I
think it should, but since I am a newbie I will leave it to you to tell me.
Re-ran with 2.7.1 because when opened R2.7.0 this AM affycoretools not
loading biomaRt for some reason. I think it may have to do that I updated
packages but I have no clue. So uninstalled 2.7.0 then installed the 2.7.1
because could not get the link for 2.7.0 to function for me. I do get some
additional warnings and errors with the 2.7.1 version that I did not see
yesterday. When I do plotPCA the legend formed correctly so I am not sure
what went wrong with the affystart. I appreciate help and any
recommendations.

Sincerely

Louisa


R version 2.7.1 (2008-06-23)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

> library(affycoretools)
Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
Loading required package: limma
Loading required package: GOstats
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: annotate
Loading required package: xtable
Loading required package: RBGL
Loading required package: Category
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: biomaRt
Loading required package: RCurl

Attaching package: 'biomaRt'


        The following object(s) are masked from package:annotate :

         getGO

Loading required package: gcrma
Loading required package: matchprobes
Loading required package: annaffy
Loading required package: KEGG.db

Attaching package: 'annaffy'


        The following object(s) are masked from package:RCurl :

         getURL
> pd <-read.AnnotatedDataFrame("pData.txt", sep="\t", header=TRUE,
row.names=1)
> dat <- ReadAffy(phenoData= pd)
> pData(dat)
               amp  trt
PolyC-1.CEL  PolyA Ctrl
PolyC-2.CEL  PolyA Ctrl
PolyC-3.CEL  PolyA Ctrl
PolyC-4.CEL  PolyA Ctrl
PolyC-5.CEL  PolyA Ctrl
PolyC-6.CEL  PolyA Ctrl
PolyC-7.CEL  PolyA Ctrl
PolyC-8.CEL  PolyA Ctrl
PolyHS-1.CEL PolyA   HS
PolyHS-2.CEL PolyA   HS
PolyHS-3.CEL PolyA   HS
PolyHS-4.CEL PolyA   HS
PolyHS-5.CEL PolyA   HS
PolyHS-6.CEL PolyA   HS
PolyHS-7.CEL PolyA   HS
PolyHS-8.CEL PolyA   HS
WTC-1.CEL       WT Ctrl
WTC-2.CEL       WT Ctrl
WTC-3.CEL       WT Ctrl
WTC-4.CEL       WT Ctrl
WTC-5.CEL       WT Ctrl
WTC-6.CEL       WT Ctrl
WTC-7.CEL       WT Ctrl
WTC-8.CEL       WT Ctrl
WTHS-1.CEL      WT   HS
WTHS-2.CEL      WT   HS
WTHS-3.CEL      WT   HS
WTHS-4.CEL      WT   HS
WTHS-5.CEL      WT   HS
WTHS-6.CEL      WT   HS
WTHS-7.CEL      WT   HS
WTHS-8.CEL      WT   HS

> eset <-affystart(groups=rep(1:4, each = 8), groupsnames =
unique(paste(pData(pd)[,1],pData(pd)[,2], sep="-")), phenoData = pd)
Background correcting
Normalizing
Calculating Expression
Please give the x-coordinate for a legend.
Please give the y-coordinate for a legend.
Error in method(paste("Density plot", plottype, sep = "."), height =
height,  :
  unused argument(s) (groupsnames = c("PolyA-Ctrl", "PolyA-HS", "WT-Ctrl",
"WT-HS"), phenoData = <S4 object of class "AnnotatedDataFrame">)
In addition: Warning messages:
1: In pca.legend(pca, groupnames, pch, col, x.coord = x.coord, y.coord =
y.coord,  :
  NAs introduced by coercion
2: In pca.legend(pca, groupnames, pch, col, x.coord = x.coord, y.coord =
y.coord,  :
  NAs introduced by coercion


> eset1 <-affystart(filenames=list.celfiles()[1:16], plot = FALSE,
pca=FALSE)
Background correcting
Normalizing
Calculating Expression
> eset2 <-affystart(filenames=list.celfiles()[17:32], plot=FALSE,
pca=FALSE)
Background correcting
Normalizing
Calculating Expression
> eset <- new("ExpressionSet", exprs=cbind(exprs(eset1), exprs(eset2)),
phenoData = pd, annotation=annotation(eset1))
Error in validObject(.Object) :
  invalid class "ExpressionSet" object: sampleNames differ between
assayData and phenoData
> sampleNames(pd)
 [1] "PolyC-1.cel"  "PolyC-2.cel"  "PolyC-3.cel"  "PolyC-4.cel"
"PolyC-5.cel"  "PolyC-6.cel"  "PolyC-7.cel"  "PolyC-8.cel"
 [9] "PolyHS-1.cel" "PolyHS-2.cel" "PolyHS-3.cel" "PolyHS-4.cel"
"PolyHS-5.cel" "PolyHS-6.cel" "PolyHS-7.cel" "PolyHS-8.cel"
[17] "WTC-1.cel"    "WTC-2.cel"    "WTC-3.cel"    "WTC-4.cel"
"WTC-5.cel"    "WTC-6.cel"    "WTC-7.cel"    "WTC-8.cel"
[25] "WTHS-1.cel"   "WTHS-2.cel"   "WTHS-3.cel"   "WTHS-4.cel"
"WTHS-5.cel"   "WTHS-6.cel"   "WTHS-7.cel"   "WTHS-8.cel"
> sampleNames(eset1)
 [1] "PolyC-1.CEL"  "PolyC-2.CEL"  "PolyC-3.CEL"  "PolyC-4.CEL"
"PolyC-5.CEL"  "PolyC-6.CEL"  "PolyC-7.CEL"  "PolyC-8.CEL"
 [9] "PolyHS-1.CEL" "PolyHS-2.CEL" "PolyHS-3.CEL" "PolyHS-4.CEL"
"PolyHS-5.CEL" "PolyHS-6.CEL" "PolyHS-7.CEL" "PolyHS-8.CEL"
> sampleNames(eset2)
 [1] "WTC-1.CEL"  "WTC-2.CEL"  "WTC-3.CEL"  "WTC-4.CEL"  "WTC-5.CEL"
"WTC-6.CEL"  "WTC-7.CEL"  "WTC-8.CEL"  "WTHS-1.CEL" "WTHS-2.CEL"
[11] "WTHS-3.CEL" "WTHS-4.CEL" "WTHS-5.CEL" "WTHS-6.CEL" "WTHS-7.CEL"
"WTHS-8.CEL"


> eset <- rma(dat)
Background correcting
Normalizing
Calculating Expression
> plotPCA(eset, groups = rep(1:4, each =8), groupnames =
unique(paste(pData(pd)[,1],pData(pd)[,2], sep="-")))