Hi all,
I have this microarray large microarray data set (ALL) from which I would like
to subset or extract a set of data based on a factor ($mol.biol). I looked
up some example of subsetting in, picked up two commands and tried both but I
got error messages as follows
> testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4"))
>> Error in c("BCR/ABL", "ALL1/AF4") : unused argument(s) ("ALL1/AF4")
> testset <- ALL[ALL$mol.biol %in% c("BCR/ABL,NEG"), ]
>> Error in ALL[ALL$mol.biol %in% c(BCR/ABL, NEG), ] :
>
>> error in evaluating the argument 'i' in selecting a method for function
>> '[': Error in c(BCR/ABL, NEG) : unused argument(s) (NEG)
At this point, I really appreciate any inputs to move forward. ….
> str(ALL)
> Formal class 'ExpressionSet' [package "Biobase"] with 7 slots
> ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots
> .. .. ..@ name : chr "Chiaretti et al."
> .. .. ..@ lab : chr "Department of Medical Oncology,
> Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women's
> Hospital, Harvard Med"| __truncated__
> .. .. ..@ contact : chr ""
> .. .. ..@ title : chr "Gene expression profile of adult T-cell
> acute lymphocytic leukemia identifies distinct subsets of patients with
> different respo"| __truncated__
> .. .. ..@ abstract : chr "Gene expression profiles were examined in
> 33 adult patients with T-cell acute lymphocytic leukemia (T-ALL). Nonspecific
> filteri"| __truncated__
> .. .. ..@ url : chr ""
> .. .. ..@ pubMedIds : chr [1:2] "14684422" "16243790"
> .. .. ..@ samples : list()
> .. .. ..@ hybridizations : list()
> .. .. ..@ normControls : list()
> .. .. ..@ preprocessing : list()
> .. .. ..@ other : list()
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"]
> with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 0 0
> ..@ assayData :<environment: 0x1078636e8>
> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"]
> with 4 slots
> .. .. ..@ varMetadata :'data.frame': 21 obs. of 1 variable:
> .. .. .. ..$ labelDescription: chr [1:21] " Patient ID" " Date of
> diagnosis" " Gender of the patient" " Age of the patient at entry" ...
> .. .. ..@ data :'data.frame': 128 obs. of 21 variables:
> .. .. .. ..$ cod : chr [1:128] "1005" "1010" "3002" "4006" ...
> .. .. .. ..$ diagnosis : chr [1:128] "5/21/1997" "3/29/2000"
> "6/24/1998" "7/17/1997" ...
> .. .. .. ..$ sex : Factor w/ 2 levels "F","M": 2 2 1 2 2 2 1 2 2
> 2 ...
> .. .. .. ..$ age : int [1:128] 53 19 52 38 57 17 18 16 15 40 ...
> .. .. .. ..$ BT : Factor w/ 10 levels "B","B1","B2",..: 3 3 5 2
> 3 2 2 2 3 3 ...
> .. .. .. ..$ remission : Factor w/ 2 levels "CR","REF": 1 1 1 1 1 1 1 1
> 1 1 ...
> .. .. .. ..$ CR : chr [1:128] "CR" "CR" "CR" "CR" ...
> .. .. .. ..$ date.cr : chr [1:128] "8/6/1997" "6/27/2000" "8/17/1998"
> "9/8/1997" ...
> .. .. .. ..$ t(4;11) : logi [1:128] FALSE FALSE NA TRUE FALSE FALSE
> ...
> .. .. .. ..$ t(9;22) : logi [1:128] TRUE FALSE NA FALSE FALSE FALSE
> ...
> .. .. .. ..$ cyto.normal : logi [1:128] FALSE FALSE NA FALSE FALSE FALSE
> ...
> .. .. .. ..$ citog : chr [1:128] "t(9;22)" "simple alt." NA
> "t(4;11)" ...
> .. .. .. ..$ mol.biol : Factor w/ 6 levels "ALL1/AF4","BCR/ABL",..: 2
> 4 2 1 4 4 4 4 4 2 ...
> .. .. .. ..$ fusion protein: Factor w/ 3 levels "p190","p190/p210",..: 3 NA
> 1 NA NA NA NA NA NA 1 ...
> .. .. .. ..$ mdr : Factor w/ 2 levels "NEG","POS": 1 2 1 1 1 1 2
> 1 1 1 ...
> .. .. .. ..$ kinet : Factor w/ 2 levels "dyploid","hyperd.": 1 1 1
> 1 1 2 2 1 1 NA ...
> .. .. .. ..$ ccr : logi [1:128] FALSE FALSE FALSE FALSE FALSE
> FALSE ...
> .. .. .. ..$ relapse : logi [1:128] FALSE TRUE TRUE TRUE TRUE TRUE ...
> .. .. .. ..$ transplant : logi [1:128] TRUE FALSE FALSE FALSE FALSE
> FALSE ...
> .. .. .. ..$ f.u : chr [1:128] "BMT / DEATH IN CR" "REL" "REL"
> "REL" ...
> .. .. .. ..$ date last seen: chr [1:128] NA "8/28/2000" "10/15/1999"
> "1/23/1998" ...
> .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"]
> with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
> ..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"]
> with 4 slots
> .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable:
> .. .. .. ..$ labelDescription: logi(0)
> .. .. ..@ data :'data.frame': 12625 obs. of 0 variables
> .. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"]
> with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
> ..@ annotation : chr "hgu95av2"
> ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"]
> with 4 slots
> .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable:
> .. .. .. ..$ labelDescription: chr(0)
> .. .. ..@ data :'data.frame': 128 obs. of 0 variables
> .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
> .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"]
> with 1 slots
> .. .. .. .. ..@ .Data:List of 1
> .. .. .. .. .. ..$ : int [1:3] 1 1 0
> ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1
> slots
> .. .. ..@ .Data:List of 4
> .. .. .. ..$ : int [1:3] 2 10 0
> .. .. .. ..$ : int [1:3] 2 5 5
> .. .. .. ..$ : int [1:3] 1 3 0
> .. .. .. ..$ : int [1:3] 1 0 0
Aki Hoji, Ph.D
Dept. Infectious Diseases & Microbiology
University of PIttsburgh
Rm427 Parran Hall, GSPH-IDM
130 Desoto St., Pittsburgh, PA 15261
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