Hello, 

 

I apologize if my question is too simple, still I would appreciate an
advice.

I am using 'Factorial Design' package for Affy Drosophila 2.0 array.

I read *.cel files using standard 'rma' way: 
>dat<-ReadAffy()
>eset <- rma(dat)
and created design for ANOVA separately in 'design.txt' file
(I have 3 populations and 2 conditions I want to analyze).
First rows of the design file are:
#-------------------------------

 

POP

ET

E1E1_DrosophilaGenome2.0.CEL

E1_2

E

E1E2_DrosophilaGenome2.0.CEL

E1_2

E

E1E5_DrosophilaGenome2.0.CEL

E1_2

E

E1W1_DrosophilaGenome2.0.CEL

E1_2

W

E1W2_DrosophilaGenome2.0.CEL

E1_2

W

E1W5_DrosophilaGenome2.0.CEL

E1_2

W

M1E1_DrosophilaGenome2.0.CEL

M1_2

E

M1E2_DrosophilaGenome2.0.CEL

M1_2

E

M1E5_DrosophilaGenome2.0.CEL

M1_2

E

M2E2_DrosophilaGenome2.0.CEL

M1_2

E

M2E5_DrosophilaGenome2.0.CEL

M1_2

E

#-------------------------------
Now, to use 'esApply' with 'lm' function as described in 'Estrogen 2x2 
factorial design' example I created a pData for eset:
pData <-read.table(file="design.txt",sep='\t',row.names=1,header=TRUE)
pData(eset)<-pData;
#-------------------------------
My question actually is: if I look now into eset object - 

> eset

ExpressionSet (storageMode: lockedEnvironment)

assayData: 18952 features, 35 samples 

  element names: exprs 

phenoData

  rowNames: E1E1_DrosophilaGenome2.0.CEL, E1E2_DrosophilaGenome2.0.CEL,
.., R2W5_DrosophilaGenome2.0.CEL (35 total)

  varLabels and varMetadata:

    POP: arbitrary numbering

    ET: arbitrary numbering

featureData

  featureNames: 1616608_a_at, 1622892_s_at, ..., AFFX-TrpnX-M_at (18952
total)

  varLabels and varMetadata: none

experimentData: use 'experimentData(object)'

Annotation [1] "drosophila2"

#-------------------------------------------

I see that  

    POP: arbitrary numbering

    ET: arbitrary numbering

 

- Does it mean that factors' levels (such as POP: E1_2, M1_2, R1_2 and
ET: E, W) are incorrectly assigned in eset object?

And another question, probably related: I had 3 levels for the factor
'POP' in "design.txt" however looking in the output of lm, I can see
only two levels - 

Call:

lm(formula = y ~ ET + POP + ET:POP)

Coefficients:

(Intercept)          ETW      POPM1_2      POPR1_2  ETW:POPM1_2
ETW:POPR1_2  

Something is definitely wrong.

And, if so, what is the correct way?

 

Best regards

Galina 

> sessionInfo()

R version 2.5.1 (2007-06-27) 

i386-pc-mingw32 

 

locale:

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

 

attached base packages:

[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"     

 

other attached packages:

       factDesign        biomaRt          RCurl            XML
RColorBrewer    drosophila2 

       "1.10.0"       "1.10.1"        "0.8-0"        "1.9-0"
"1.0-1"       "1.16.0" 

      multtest       survival drosophila2cdf           affy
affyio        Biobase 

      "1.16.1"         "2.32"       "1.16.0"       "1.14.2"
"1.4.1"       "1.14.1"


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