Cannot able to find a particular column in R

Question

[xxxxxxxx]

While importing data from a database(ArrayExpress) using this -

anno_AE <- getAE("accessionid", path = raw_data_dir, type = "raw")
sdrf_location <- file.path(raw_data_dir, "accessionid.sdrf.txt")
SDRF <- read.delim(sdrf_location, stringsAsFactors = FALSE)
rownames(SDRF) <- SDRF$Array.Data.File

After this-

SDRF <- AnnotatedDataFrame(SDRF)

Cannot able to find column 'Array.data.file' in SDRF

How to solve this issue?

[cpad0112]

can you post output from colnames(SDRF) here?

I am confused after finding similar question on https://stackoverflow.com/questions/67514240/gpr-txt-really-a-cel-file-error-in-read-celfile-headerx by xyzzz. This post has different input for rownames(SDRF) compared to here, but rest of the content is same.

in this post: rownames(SDRF) <- SDRF$Array.Data.File

In SO post; rownames(SDRF) <- make.unique(SDRF$Array.Data.File)

Please note that the volunteers here spend their time to address an issue and please respect their time.

[xxxxxxxx]

colnames(SDRF) <- SDRF$Array.Data.File

Error in names(x) <- value : 'names' attribute [192] must be the same length as the vector [41]

[cpad0112]

SDRF <- read.delim(sdrf_location, stringsAsFactors = FALSE)
colnames(SDRF)

Please post the output from colnames(SDRF)

[xxxxxxxx]

colnames(SDRF)



[1] "Source.Name"                                    
 [2] "Characteristics..Organism."                     
 [3] "Term.Source.REF"                                
 [4] "Term.Accession.Number"                          
 [5] "Characteristics..CellLine."                     
 [6] "Term.Source.REF.1"                              
 [7] "Term.Accession.Number.1"                        
 [8] "Characteristics..TargetedCellType."             
 [9] "Protocol.REF"                                   
[10] "Protocol.REF.1"                                 
[11] "Sample.Name"                                    
[12] "Protocol.REF.2"                                 
[13] "Parameter.Value..Amplification."                
[14] "Parameter.Value..Extracted.product."            
[15] "Protocol.REF.3"                                 
[16] "Extract.Name"                                   
[17] "Material.Type"                                  
[18] "Protocol.REF.4"                                 
[19] "Parameter.Value..Amplification..1"              
[20] "Parameter.Value..Label.used."                   
[21] "Labeled.Extract.Name"                           
[22] "Label"                                          
[23] "Material.Type.1"                                
[24] "Protocol.REF.5"                                 
[25] "Parameter.Value..Chamber.type."                 
[26] "Parameter.Value..Quantity.of.label.target.used."
[27] "Unit..MassUnit."                                
[28] "Parameter.Value..temperature."                  
[29] "Unit..TemperatureUnit."                         
[30] "Hybridization.Name"                             
[31] "Array.Design.REF"                               
[32] "Protocol.REF.6"                                 
[33] "Factor.Value..infect."                          
[34] "Factor.Value..time."                            
[35] "Unit..TimeUnit."                                
[36] "Scan.Name"                                      
[37] "Array.Data.File"                                
[38] "Comment..ArrayExpress.FTP.file."                
[39] "Protocol.REF.7"                                 
[40] "Derived.Array.Data.Matrix.File"                 
[41] "Comment..Derived.ArrayExpress.FTP.file."        
> 

[zx8754]

Maybe check the spelling you have [37] "Array.Data.File", and it expects "Array.data.file"

[xxxxxxxx]

when I am trying to write this -

raw_data <- oligo::read.celfiles(filenames = file.path(raw_data_dir, SDRF$

after $ when I click on tab it is not showing the colnames?

[cpad0112]

Thanks for posting the colnames output. can you post output from SDRF$Array.Data.File here? Btw, is there any reason why AnnotatedDataframe is built from only one dataframe unless you are supplying phenodata elsewhere? My understanding is that it is created from data frame and corresponding metadata. In addition open your accessionid.sdrf.txt and check the entries under Array.Data.File column. They must all be cel files. If you have checked the E-MTAB-2967.sdrf.txt mentioned in the tutorial you are following, you would find only cel files in that column.