NimbleGen MicroArray Analysis via ArrayExpress Data base
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6.4 years ago
morovatunc ▴ 510

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

>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

nimblegen ArrayExpress Microarray Bioconductor • 2.0k views
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6.4 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.

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