Question: affylmGUI affy affymetrix
0
gravatar for gtrdy20
4.0 years ago by
gtrdy200
gtrdy200 wrote:

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 • 604 views
ADD COMMENTlink modified 4.0 years ago by Gordon Smyth39k • written 4.0 years ago by gtrdy200
Answer: affylmGUI affy affymetrix
0
gravatar for Gordon Smyth
4.0 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

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?

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Gordon Smyth39k

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

I 'm gonna try it now.

Thanks !

ADD REPLYlink written 4.0 years ago by gtrdy200

Dear Gordon,

Thanks for your useful help.

It worked :)

 

ADD REPLYlink written 4.0 years ago by gtrdy200
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