Cannot read Illumina data (.bgx and .txt format) in R for microanalysis

Question

[deeptivipin]

Hi All!

This is my first time with Illumina datasets and I'm stuck near loading data. My files are in . bgx and .txt format and they are not being read in limma, lumi and beadarray in R-v 3.1.1. It shows errors as follows both file types:

lumi:

Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds

limma:

Error in readGenericHeader(fname, columns = expr, sep = sep) :
  Specified column headings not found in file

Would really appreciate your help.

Thanks in advance!

PS: link to the txt file

[Sean Davis]

You'll probably have to share at least a few lines of the txt file for us to make any suggestions.

[deeptivipin]

Thanks Sean!

I've added a link to download the file.

[Zhilong Jia]

Any solution found?

[deeptivipin]

Yes. I found that my firewall was blocking the download after all.

Answer 1

[Sean Davis]

Your txt is a file from NCBI GEO. The easiest way to get data from GEO into R is to use the GEOquery package.

library(GEOquery)
eset = getGEO('GSE28985')[[1]]

Now, eset is an ExpressionSet and you can use it with limma, etc. See the Biobase vignette describing ExpressionSets if you want more detail.

[deeptivipin]

I tried GEOquery as you mentioned. Still showing the same error.

[Sean Davis]

So, if you run the code in my answer, you get an error? Or were you using some other code? If it was something else, what did you type and what was the error?

[deeptivipin]

I ran the codes that you gave after installing package limma. It showed the following:

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28985/matrix/
Found 1 file(s)
GSE28985_series_matrix.txt.gz
Using locally cached version: C:\Users\DEEPTI\AppData\Local\Temp\Rtmpa4JYMi/GSE28985_series_matrix.txt.gz
Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  invalid 'nlines' argument

[Sean Davis]

And what is the output of sessionInfo() after loading the GEOquery library?

[deeptivipin]

Actually this was the initial result to

eset = getGEO('GSE28985')[[1]]

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28985/matrix/
Found 1 file(s)
GSE28985_series_matrix.txt.gz
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28985/matrix/GSE28985_series_matrix.txt.gz'
using Synchronous WinInet calls
Error in download.file(sprintf("ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  : 
  cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28985/matrix/GSE28985_series_matrix.txt.gz'
In addition: Warning message:
In download.file(sprintf("ftp://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  InternetOpenUrl failed: 'The FTP session was terminated

When I tried it again I got what I posted above

The output for sessionInfo() is

R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                   LC_TIME=English_India.1252    

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

other attached packages:
[1] limma_3.20.8        GEOquery_2.30.1     affy_1.42.3         Biobase_2.24.0      BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] affyio_1.32.0         BiocInstaller_1.14.2  preprocessCore_1.26.1 RCurl_1.95-4.3       
[5] tools_3.1.0           XML_3.98-1.1          zlibbioc_1.10.0     



R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                   LC_TIME=English_India.1252    

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

other attached packages:
[1] limma_3.20.8        GEOquery_2.30.1     affy_1.42.3         Biobase_2.24.0      BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] affyio_1.32.0         BiocInstaller_1.14.2  preprocessCore_1.26.1 RCurl_1.95-4.3       
[5] tools_3.1.0           XML_3.98-1.1          zlibbioc_1.10.0

[salamandra]

this gets you already normalized data. how do you get raw data from txt file?

[Sean Davis]

Downloading the supplemental files from the GEO website (or using GEOquery) will get you the files. From there, you'll have to determine the best way to parse them.