Problem with ArrayExpress() command. Please help ..

Question

[Pijush Das]

I an new in micro array data analysis. I want to do the differential expression analysis of an Array Express data set (E-UMCU-11). But when I am using the command "AEset = ArrayExpress("E-UMCU-11") " The error given below is coming. I try to find out the solution in net and found "How to get the expression data of each gene from the ArrayExpress database.", Then I try to use E-UMCU-11.eSet.r but there is no such file with E-UMCU-11 data set. Please help me ..

The error is given below:

AEset = ArrayExpress("E-UMCU-11")

AEset = ArrayExpress("E-UMCU-11") trying URL 'http://www.ebi.ac.uk/arrayexpress/files/A-UMCU-3/A-UMCU-3.adf.txt' Content type 'text/plain' length 1202947 bytes (1.1 Mb) opened URL downloaded 1.1 Mb

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-UMCU-11/E-UMCU-11.sdrf.txt' Content type 'text/plain' length 398344 bytes (389 Kb) opened URL downloaded 389 Kb

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-UMCU-11/E-UMCU-11.idf.txt' Content type 'text/plain' length 22128 bytes (21 Kb) opened URL downloaded 21 Kb

Copying raw data files

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-UMCU-11/E-UMCU-11.raw.1.zip' Content type 'application/zip' length 183874288 bytes (175.4 Mb) opened URL downloaded 175.4 Mb

trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-UMCU-11/E-UMCU-11.raw.2.zip' Content type 'application/zip' length 74188350 bytes (70.8 Mb) opened URL downloaded 70.8 Mb

Unpacking data files ArrayExpress: Reading pheno data from SDRF ArrayExpress: Reading data files Error in getDataColsForAE1(path, files) : No scanner name is given. It is not possible to handle such a case. Try to set the argument 'dataCols' by choosing >among the following columns names: "MetaRow" "MetaColumn" "Row" "Column" "mean signal Cy5" "mean background Cy5" "median signal Cy5" "median background Cy5" "standard deviation signal Cy5" "standard deviation background Cy5" "mean signal Cy3" "mean background Cy3" "median signal Cy3" "median background Cy3" "standard deviation signal Cy3" "standard deviation background Cy"

ArrayExpress: Reading feature metadata from ADF Read 65 items Error : object 'raweset' not found

Answer 1

[deepue]

I have faced the below error when tried to download the experiment.

Error in `row.names<-.data.frame`(`*tmp*`, value = c("E-UMCU-11_161_Measured1.txt",  : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘E-UMCU-11_1_Measured1.txt’, ‘E-UMCU-11_10_Measured1.txt’, ‘E-UMCU-11_100_Measured1.txt’, ‘E-UMCU-11_101_Measured1.txt’, ‘E-UMCU-11_102_Measured1.txt’, ‘E-UMCU-11_103_Measured1.txt’, ‘E-UMCU-11_104_Measured1.txt’, ‘E-UMCU-11_105_Measured1.txt’, ‘E-UMCU-11_106_Measured1.txt’, ‘E-UMCU-11_107_Measured1.txt’, ‘E-UMCU-11_108_Measured1.txt’, ‘E-UMCU-11_109_Measured1.txt’, ‘E-UMCU-11_11_Measured1.txt’, ‘E-UMCU-11_110_Measured1.txt’, ‘E-UMCU-11_111_Measured1.txt’, ‘E-UMCU-11_112_Measured1.txt’, ‘E-UMCU-11_113_Measured1.txt’, ‘E-UMCU-11_114_Measured1.txt’, ‘E-UMCU-11_115_Measured1.txt’, ‘E-UMCU-11_116_Measured1.txt’, ‘E-UMCU-11_117_Measured1.txt’, ‘E-UMCU-11_118_Measured1.txt’, ‘E-UMCU-11_119_Measured1.txt’, ‘E-UMCU-11_12_Measured1.txt’, ‘E-UMCU-11_120_Measured1.txt’, ‘E-UMCU-11_121_Measured1.txt’, ‘E-UMCU-11_122_Measured1.txt’, ‘E-UMCU-11_123 [... truncated] 
NULL

The row names should not be duplicated, as expected by the function. Try contacting ArrayExpress.