NimbleGen MicroArray Analysis via ArrayExpress Data base
Entering edit mode
8.8 years ago
morovatunc ▴ 550


I am trying to analyse E-MTAB-1956 coded array express data set. For nimblegen microarray data analysis, I have used oligo package, thus xys files. However, Array express has .pair formatted data.

1) Is there any way that I can only do analyse with .pair data?

2) I have followed manual of ArrayExpress package( from bioconductor) in order to analyse with the package's way. But, I have come across with loading data from the source. The non-affy method that I have used, did not even give me object that contains rawdata.

Let me share the code that I have written very below. It somehow does not find the data column. Even I, give it as a argument such as dataCols ='PM' (since in pair data intensities of PM col is taken account)

3) Finally, ArrayEpress gives the annotation file as a format of .adf . It is different than .ndf file? how can I transform .adf to ndf? or How can I use .adf for the analyse.

I appreciate your help very much. I would be more than glad. Thank you!

best regards


> infodata = getAE("E-MTAB-1956", type = "full")
> infodata

[1] "/Volumes/MyPassport/MyProjects/FertilityProject/Veriler"

[1] "419231A01_2011-07-06_10-35_scan_532.pair" "419231A02_2011-07-06_10-35_scan_532.pair"
[3] "419231A03_2011-07-06_10-35_scan_532.pair" "419231A04_2011-07-06_10-35_scan_532.pair"
[5] "414993A01_2011-07-06_10-48_scan_532.pair" "414993A02_2011-07-06_10-48_scan_532.pair"
[7] "414993A03_2011-07-06_10-48_scan_532.pair" "414993A04_2011-07-06_10-48_scan_532.pair"

[1] ""



[1] "E-MTAB-1956.sdrf.txt"

[1] "E-MTAB-1956.idf.txt"

[1] "A-MEXP-1785.adf.txt"

> cn = getcolproc(infodata)

Error in if (file == "") file <- stdin() else { :
  argument is of length zero
In addition: Warning message:
In getcolproc(infodata) : Unable to find Derived Data column in SDRF
Microarray Bioconductor ArrayExpress nimblegen • 2.5k views
Entering edit mode
8.8 years ago
matt.newman ▴ 170

I can only help for the first part. If you want to do a trial, download our gene expression analysis software (Array Studio). We support Nimblegen data, although I seem to remember having an ndf format. Anyway, you could potentially use the trial version of our software to just transform the data, then export it back to R.

Entering edit mode

Thank you very much for your advice Sir! I will try your program.


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