NimbleGen MicroArray Analysis via ArrayExpress Data base

Question

[morovatunc]

Hello,

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

Tunc

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

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

$rawFiles
[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"

$rawArchive
[1] "E-MTAB-1956.raw.1.zip"

$processedFiles
NULL

$processedArchive
NULL

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

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

$adf
[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

Answer 1

[matt.newman]

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.

[morovatunc]

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