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Robin: Agilent 44K file import

Robin: Agilent 44K file import
Answer
5/10/10 3:59 PM
hi,
first, great job and thank you for developing Robin!
This tool will be definitely very useful for many scientists

now I would like to import some Agilent 44K raw data files as generic tabular, but unfortunately "the layout I'va entered is not fitting to the number of data rows in the input". I choose Agilent 44K for both Import presets and Chip Layout, the number of rows and cols is resp. 532 and 85 in my files...
how can I modify the original file to be imported?

thank you a lot ;)

RE: Robin: Agilent 44K file import
Answer
5/10/10 8:28 PM as a reply to Sébastien Wieckowski.
Hi,
and thanks for your interest in Robin. When importing Agilent data you
should not specify the format as being generic tabular but as being "Agilent" -
this option should be shown directly above the "generic tabular" option when
choosing the generic single channel or two color workflow. If this option is not
displayed you might have an earlier version installed (the version number is
displayed in the window title bar - the latest version is 1.1.1RC6) - please download
the latest version from http://mapman.gabipd.org/web/guest/robin

I hope this solves your problems,
best greetings,
Marc

RE: Robin: Agilent 44K file import
Answer
5/11/10 2:48 PM as a reply to Marc Lohse.
hi Marc,

thank you for helping me

I have the latest version of Robin and tried to import my Agilent raw data as you mentioned, but unfortunately problem still remains (please see attached file)
the import presets work fine as the required colums were detected, but there is something wrong with the chip layout...
I already tried to delete all the sections before the first data point in the original file (TYPE, FEPARAMS, DATA,*, TYPE, STATS, DATA, *, TYEP, and FEATURES sections) but it was not better...
I also checked that the latest data point is at position 532x85
what about the grid rows and colums parameters in the lower part of the import window?

thank you for your help
Sébastien

RE: Robin: Agilent 44K file import
Answer
5/14/10 3:16 PM as a reply to Sébastien Wieckowski.
Hi Sébastien,

this really sounds strange since it looks like your data files are complete. Did you check whether all
the data files do actually contain the 532x85 data rows? I am asking that because it seems like Agilent
is sometimes intentionally removing data rows from the raw files because these contain control probes
that have been masked out. If one file in your set was masked out and does not contain the 532x85 rows
it would explain the error message.

Bests,
Marc

RE: Robin: Agilent 44K file import
Answer
5/17/10 12:06 PM as a reply to Marc Lohse.
Hi Marc, and thank you for your patience

you are right, some points are missing in the files... actually only 5 points are missing, but "structural" data points like negative controls and bright/dark corners are still included

I am novice in this field, and got the files from Miltenyi microarray service...
I will try to add manually missing rows

thanks a lot!

Sébastien

RE: Robin: Agilent 44K file import
Answer
5/17/10 12:35 PM as a reply to Sébastien Wieckowski.
Hi Sébastien,

unfortunately Robin is (has to) be that pedantic when loading the data - the number of
data points in the files has to exactly match the design. Adding the five missing lines in
your case and giving them some dummy identifier should do no harm and enable you
to analyse your data with Robin. Since we now know this potential problem with Agilent
data we will consider adding some automatic padding function to the Agilent importer.

cheers,
Marc

RE: Robin: Agilent 44K file import
Answer
5/17/10 3:35 PM as a reply to Marc Lohse.
ok, it works fine and Robin can now import my files
I copied the data line 'BrightCorner' (the very first data point) to missing rows, and adjusted the row (and line) as well as the FeatureNum values
I had to play with MS Excel ;)

thanks a lot!

Sébastien