readIllumina couln't read bead-level txt file from GEO raw data
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gnilihzeux • 0
@gnilihzeux-9874
Last seen 6.6 years ago

Hello everyone,I have been struggling to the problem about how to read in bead-level txt file provided by GEO using beadarray::readIllumina, but I have no more idea to solve this.

The documents by beadarray didn't show an example for bead-level txt but other formats such as .bab and .tiff in 'BeadArrayUseCases'.

My data from GEO raw data is as follows:

#file: GSM1105686_8839265065_J.txt
#format
Code    Grn    GrnX    GrnY
10008    2530    697.5355    3672.499
10008    2881    1112.538    6927.974
<font face="sans-serif, Arial, Verdana, Trebuchet MS">
</font>

My error is as follows:

Warning messages:
1: Unknown input format in fileD:\test\GSE45495\1/8839265065_J.txt
  This is probably not a bead-level text file and was ignored

My sessionInfo:

R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] beadarrayExampleData_1.8.0 beadarray_2.20.1          
[3] ggplot2_2.1.0              Biobase_2.30.0            
[5] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3          AnnotationDbi_1.32.3 XVector_0.10.0      
 [4] magrittr_1.5         GenomicRanges_1.22.4 zlibbioc_1.16.0     
 [7] IRanges_2.4.8        munsell_0.4.3        colorspace_1.2-6    
[10] stringr_1.0.0        plyr_1.8.3           GenomeInfoDb_1.6.3  
[13] tools_3.2.2          base64_1.1           grid_3.2.2          
[16] gtable_0.2.0         DBI_0.3.1            reshape2_1.4.1      
[19] S4Vectors_0.8.11     RSQLite_1.0.0        limma_3.26.8        
[22] stringi_1.0-1        BeadDataPackR_1.22.0 scales_0.4.0        
[25] stats4_3.2.2         illuminaio_0.12.0   

The solution I could think of is using 'Bioconductor:lumi' to read in 'array_address_id' and 'intensity' and then preprocess to get the final expression profile.

beadarray bead-level GEO lumi • 996 views
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Entering edit mode
Mike Smith ★ 5.7k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg / de.NBI

I just downloaded the data, and it looks like all the bead-level text files have a header that isn't normally there:

# Supplementary beadlevel raw data file
Code    Grn    GrnX    GrnY
10008    2530    697.5355    3672.499
10008    2881    1112.538    6927.974
10008    2245    1617.493    11434.48
10008    2333    588.6597    7040.719

If you remove  the line that says '# Supplementary beadlevel raw data file', beadarray should be able to read them in. It's pretty rare to find bead-level data in GEO, so I don't know why that line has been inserted into the files, but if this turns into a frequent problem we'll handle in the package. For now I suggest just manually editing the files.

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Entering edit mode

Thank you very much! It suffers me for a long time but it is an unexpected solution. By the way, whether if it is a right way that I preprocess the data using just two columns 'Code' and ‘Grn' by lumi?

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