[R] A problem subsetting a data frame

[Aki Hoji]

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