affylmGUI affy affymetrix
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gtrdy20 • 0
@gtrdy20-9293
Last seen 6.5 years ago

Hi everyone

I 'm new to R! I 'm starting to work on my affymetrix data from GPL570 in R using affylmGUI.

when loading my data after loading Targets file, immediately I get these three errors :

1. Is GSM397626.CEL really a cell file ? tried reading as text, gzipped text, binary,gzipped binary, command console and gzipped command console formats.

2.error in assign ("Rawaffydata", rawaffydata, affylmGUIenvironment): object ''rawaffydata'' not found.

3.error in colnames(expres(rawaffydata)):

error in evaluating the argument 'x' in selecting a method for function 'colnames': error in expres(rawaffydata):

error in evaluating the argument 'object' in selecting a method for function 'expres': error:object 'rawaffydata' not found.

Thanks in advance.

Maria

affylmgui • 904 views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Well, your file GSM397626.CEL is apparently corrupted. Try downloading it again. It should be about 13MB in size.

The GEO sample GSM397626 is part of GEO series GSE15824, which contains 45 samples in total:

   http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15824

Have you created a directory with all 45 CEL files in it?

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I have only 14 samples in directory. Let me download the rest of the data. 

I 'm gonna try it now.

Thanks !

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Dear Gordon,

Thanks for your useful help.

It worked :)

 

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