Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2014-01-12 Thread ndigirol 

Dear Henrik, 

Thank you so much for your help, providing the information and links!
Problem is solved.

Niki

On Saturday, January 11, 2014 1:37:51 PM UTC-5, Henrik Bengtsson wrote:
>
> On Sat, Jan 11, 2014 at 4:59 AM,  > 
> wrote: 
> > Hi Jerry, 
> > 
> > Have you been able to resolve this issue? 
> > I ran into the same problem while working with matlab: 
>
> What's this sudden interest from the Matlab side and which Matlab 
> toolbox is the source of all this? 
> > 
> > Warning: The ChipType (Mouse430_2) of CEL file GSM315892.cel does not 
> > match the ChipType (Mouse430A_2) of library file Mouse430A_2.CDF. 
> > In celintensityread at 248 
> > Error using celintensityread (line 253) 
> > The Rows (1002) or Cols(1002) of CEL file GSM315892.cel does not match 
> the 
> > Rows (732) or Cols(732) of library file Mouse430A_2.CDF. Please check 
> the 
> > files are the correct. 
>
> As the message clearly indicates 'Mouse430_2' and 'Mouse430A_2' are 
> two different chip types.  As I wrote in my previous message to this 
> thread, the terms "CDF" and "chip type" must not be used 
> interchangeably, 
> cf. http://aroma-project.org/definitions/chipTypesAndCDFs.  It is 
> important to understand the difference. 
>
> /Henrik 
>
> > 
> > Please let me know! 
> > Thank you and have a nice weekend! 
> > 
> > Niki 
> > 
> > -- 
> > -- 
> > When reporting problems on aroma.affymetrix, make sure 1) to run the 
> latest 
> > version of the package, 2) to report the output of sessionInfo() and 
> > traceback(), and 3) to post a complete code example. 
> > 
> > 
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Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2014-01-11 Thread Henrik Bengtsson 
On Sat, Jan 11, 2014 at 4:59 AM,   wrote:
> Hi Jerry,
>
> Have you been able to resolve this issue?
> I ran into the same problem while working with matlab:

What's this sudden interest from the Matlab side and which Matlab
toolbox is the source of all this?
>
> Warning: The ChipType (Mouse430_2) of CEL file GSM315892.cel does not
> match the ChipType (Mouse430A_2) of library file Mouse430A_2.CDF.
> In celintensityread at 248
> Error using celintensityread (line 253)
> The Rows (1002) or Cols(1002) of CEL file GSM315892.cel does not match the
> Rows (732) or Cols(732) of library file Mouse430A_2.CDF. Please check the
> files are the correct.

As the message clearly indicates 'Mouse430_2' and 'Mouse430A_2' are
two different chip types.  As I wrote in my previous message to this
thread, the terms "CDF" and "chip type" must not be used
interchangeably,
cf. http://aroma-project.org/definitions/chipTypesAndCDFs.  It is
important to understand the difference.

/Henrik

>
> Please let me know!
> Thank you and have a nice weekend!
>
> Niki
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
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Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2014-01-11 Thread Henrik Bengtsson 
On Sat, Nov 2, 2013 at 10:48 AM,   wrote:
> Hi Philip,
>
>
>
> Thank you for your reply.  OK, understood.  However, FYI, I have applied
> "affyrma" as well, and again I got following error.  Also, I am using this
> binary CDF (HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1) that
> its size is ~17 MB.
>
>
>
> Warning: The ChipType (HuGene-1_1-st-v1) of CEL file
>
> 053111_Proof_43B005ZN-AB_HuGene1.1ST_C05_2.CEL does not match the ChipType
>
> (HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1) of library file
>
> HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.CDF.


VERY USEFUL TO UNDERSTAND:

1. The terms "CDF" and "chip type" must not be used interchangeably,
cf. http://aroma-project.org/definitions/chipTypesAndCDFs
2. The *chip type* of a *CEL* file is stored in the header of the CEL
file and therefore inferred from the *content* CEL file.
3. The chip type of a *CDF* file is *not* stored in the file itself.
It can at best be inferred from the *filename* of the CDF file.  (If
Affymetrix had added a header to the CDF file format when they
designed it, things would not be this complicated).

4. In *aroma.affymetrix*, the chip type is inferred from the CDF
filename by (i) dropping the filename extension and then (ii) dropping
everything after the first comma (called tags, cf.
http://aroma-project.org/definitions/namesAndTags).  For example, for
'HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.CDF',
*aroma.affymetrix* will infer/assume that the *chip type* is
HuGene-1_1-st-v1.

5. Using CDF with (aroma-style) comma-separated tags in their
filenames in other software, will most likely not work, because those
tools most likely infer the chip type from the full filename.  That
is, they will believe the chip type is
'HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1' - just as
the above warnings.

Thus, in order to use those CDF files in other software, you need to
manually remove the comma-separated tags from the filename so that
they are named 'HuGene-1_1-st-v1.CDF', or by other means tell the
software that what the proper chip type is for that CDF.  Rhetorical
sarcasm: Now, good luck keeping track of different types/versions of
CDFs for the same chip type - which is avoided when using
aroma.affymetrix where you can add tags to the CDF filenames.

>
>> In celintensityread at 255
>
>   In affyrma at 98

This I consider a non-aroma.affymetrix question; please contact the
author whatever Matlab package you are using.

/Henrik

>
> Thanks,
> Jerry
>
>
>
>
>
> On Saturday, November 2, 2013 9:20:03 AM UTC-7, Guido wrote:
>>
>> Hi Jerry,
>>
>> Let me first say this: it is impossible for me/Philip to track the problem
>> down since we don't have any experience with the analysis of Affymetrix
>> arrays using Matlab. We standardly use R/BioC/aroma.affymetrix.
>> However, I noticed you try to perform gcrma normalization. Since the ST
>> arrays consist of PM probes only, GCRMA normalization won't work. What
>> happens if you try to RMA-normalize your data (using "affyrma" in Matlab)?
>>
>> Regards,
>> Guido
>> ________________
>> From: jerry...@gmail.com [jerry...@gmail.com]
>> Sent: Saturday, November 02, 2013 12:29 AM
>> To: aroma-af...@googlegroups.com
>> Cc: jerry...@gmail.com; Hooiveld, Guido
>> Subject: Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array
>>
>> Hi Philip,
>> Thank you for your reply.  I am using MATLAB to analyze the gene
>> expression data generated by "Affymetrix Human Gene 1.1-ST Array".  When I
>> ran this function “affygcrma”, I got following error:
>>
>> Warning: The ChipType (HuGene-1_1-st-v1) of CEL file
>> ASFREYT_HuGene1.1ST_C04_2.CEL does not match the ChipType
>> (HuGene-1_1-st-v1_ascii) of library file HuGene-1_1-st-v1_ascii.CDF.
>> > In celintensityread at 255
>>   In affygcrma at 140
>>
>> Thanks,
>> Jerry
>>
>> On Friday, November 1, 2013 3:20:09 PM UTC-7, philipg wrote:
>> Hi Jerry,
>>
>> I read your message regarding the binary CDF that you downloaded from
>> NuGO_R.html (I am responsible for these packages and I am the maintainer of
>> NuGO_R.html). Unfortunately, you are not explaining what exactly the
>> problems are that you encounter? Can you please explain to me what you are
>> trying to do and in what kind of problems you run? I'll try to give you a
>> hand then.
>>
>> Regards,
>>
>> Philip de Groot
>> Wageningen University
>>
>>
>> 2013/11/1 
>> Hello,
>>
>> To analyze Human Gene 1.1 st array, I

Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2014-01-11 Thread ndigirol 
Hi Jerry,

Have you been able to resolve this issue?
I ran into the same problem while working with matlab:

Warning: The ChipType (Mouse430_2) of CEL file GSM315892.cel does not
match the ChipType (Mouse430A_2) of library file Mouse430A_2.CDF.
In celintensityread at 248 
Error using celintensityread (line 253)
The Rows (1002) or Cols(1002) of CEL file GSM315892.cel does not match the
Rows (732) or Cols(732) of library file Mouse430A_2.CDF. Please check the
files are the correct.

Please let me know!
Thank you and have a nice weekend!

Niki 

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-- 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2013-11-02 Thread jerrycholo 
 

Hi Philip,

 

Thank you for your reply.  OK, understood.  However, FYI, I have applied 
"affyrma" as well, and again I got following error.  Also, I am using this 
binary CDF (HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1) that 
its size is ~17 MB.

 

Warning: The ChipType (HuGene-1_1-st-v1) of CEL file

053111_Proof_43B005ZN-AB_HuGene1.1ST_C05_2.CEL does not match the ChipType

(HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1) of library file

HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.CDF. 

> In celintensityread at 255

  In affyrma at 98

Thanks,
Jerry

 

 
On Saturday, November 2, 2013 9:20:03 AM UTC-7, Guido wrote:

> Hi Jerry, 
>
> Let me first say this: it is impossible for me/Philip to track the problem 
> down since we don't have any experience with the analysis of Affymetrix 
> arrays using Matlab. We standardly use R/BioC/aroma.affymetrix. 
> However, I noticed you try to perform gcrma normalization. Since the ST 
> arrays consist of PM probes only, GCRMA normalization won't work. What 
> happens if you try to RMA-normalize your data (using "affyrma" in Matlab)? 
>
> Regards, 
> Guido   
>  
> From: jerry...@gmail.com  [jerry...@gmail.com ] 
> Sent: Saturday, November 02, 2013 12:29 AM 
> To: aroma-af...@googlegroups.com  
> Cc: jerry...@gmail.com ; Hooiveld, Guido 
> Subject: Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array 
>
> Hi Philip, 
> Thank you for your reply.  I am using MATLAB to analyze the gene 
> expression data generated by "Affymetrix Human Gene 1.1-ST Array".  When I 
> ran this function “affygcrma”, I got following error: 
>
> Warning: The ChipType (HuGene-1_1-st-v1) of CEL file 
> ASFREYT_HuGene1.1ST_C04_2.CEL does not match the ChipType 
> (HuGene-1_1-st-v1_ascii) of library file HuGene-1_1-st-v1_ascii.CDF. 
> > In celintensityread at 255 
>   In affygcrma at 140 
>
> Thanks, 
> Jerry 
>
> On Friday, November 1, 2013 3:20:09 PM UTC-7, philipg wrote: 
> Hi Jerry, 
>
> I read your message regarding the binary CDF that you downloaded from 
> NuGO_R.html (I am responsible for these packages and I am the maintainer of 
> NuGO_R.html). Unfortunately, you are not explaining what exactly the 
> problems are that you encounter? Can you please explain to me what you are 
> trying to do and in what kind of problems you run? I'll try to give you a 
> hand then. 
>
> Regards, 
>
> Philip de Groot 
> Wageningen University 
>
>
> 2013/11/1  
> Hello, 
>
> To analyze Human Gene 1.1 st array, I used these CDF files, which are: 
> HuGene-1_1-st-v1_ascii.CDF (from affymetrix) and (ii) 
> HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.cdf (from 
> http://nmg-r.bioinformatics.nl/NuGO_R.html).  Unfortunately, I am getting 
> errors that stop me to move forward in my work.  Please let me know if 
> there is another website to download this CDF file. 
> Thanks, 
> Jerry 
>
> -- 
> -- 
> When reporting problems on aroma.affymetrix, make sure 1) to run the 
> latest version of the package, 2) to report the output of sessionInfo() and 
> traceback(), and 3) to post a complete code example. 
>
>
> You received this message because you are subscribed to the Google Groups 
> "aroma.affymetrix" group with website http://www.aroma-project.org/. 
> To post to this group, send email to aroma-af...@googlegroups.com 
> To unsubscribe and other options, go to 
> http://www.aroma-project.org/forum/ 
>
> --- 
> You received this message because you are subscribed to the Google Groups 
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>
>
>

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RE: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2013-11-02 Thread Hooiveld, Guido 
Hi Jerry,

Let me first say this: it is impossible for me/Philip to track the problem down 
since we don't have any experience with the analysis of Affymetrix arrays using 
Matlab. We standardly use R/BioC/aroma.affymetrix.
However, I noticed you try to perform gcrma normalization. Since the ST arrays 
consist of PM probes only, GCRMA normalization won't work. What happens if you 
try to RMA-normalize your data (using "affyrma" in Matlab)?

Regards,
Guido  

From: jerrych...@gmail.com [jerrych...@gmail.com]
Sent: Saturday, November 02, 2013 12:29 AM
To: aroma-affymetrix@googlegroups.com
Cc: jerrych...@gmail.com; Hooiveld, Guido
Subject: Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

Hi Philip,
Thank you for your reply.  I am using MATLAB to analyze the gene expression 
data generated by "Affymetrix Human Gene 1.1-ST Array".  When I ran this 
function “affygcrma”, I got following error:

Warning: The ChipType (HuGene-1_1-st-v1) of CEL file
ASFREYT_HuGene1.1ST_C04_2.CEL does not match the ChipType
(HuGene-1_1-st-v1_ascii) of library file HuGene-1_1-st-v1_ascii.CDF.
> In celintensityread at 255
  In affygcrma at 140

Thanks,
Jerry

On Friday, November 1, 2013 3:20:09 PM UTC-7, philipg wrote:
Hi Jerry,

I read your message regarding the binary CDF that you downloaded from 
NuGO_R.html (I am responsible for these packages and I am the maintainer of 
NuGO_R.html). Unfortunately, you are not explaining what exactly the problems 
are that you encounter? Can you please explain to me what you are trying to do 
and in what kind of problems you run? I'll try to give you a hand then.

Regards,

Philip de Groot
Wageningen University


2013/11/1 
Hello,

To analyze Human Gene 1.1 st array, I used these CDF files, which are: 
HuGene-1_1-st-v1_ascii.CDF (from affymetrix) and (ii) 
HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.cdf (from 
http://nmg-r.bioinformatics.nl/NuGO_R.html).  Unfortunately, I am getting 
errors that stop me to move forward in my work.  Please let me know if there is 
another website to download this CDF file.
Thanks,
Jerry

--
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2013-11-01 Thread jerrycholo 
 

Hi Philip,

Thank you for your reply.  I am using MATLAB to analyze the gene expression 
data generated by "Affymetrix Human Gene 1.1-ST Array".  When I ran this 
function “affygcrma”, I got following error:

Warning: The ChipType (HuGene-1_1-st-v1) of CEL file
ASFREYT_HuGene1.1ST_C04_2.CEL does not match the ChipType
(HuGene-1_1-st-v1_ascii) of library file HuGene-1_1-st-v1_ascii.CDF. 
> In celintensityread at 255
  In affygcrma at 140

Thanks,
Jerry

On Friday, November 1, 2013 3:20:09 PM UTC-7, philipg wrote:

>   Hi Jerry,
>
> I read your message regarding the binary CDF that you downloaded from 
> NuGO_R.html (I am responsible for these packages and I am the maintainer of 
> NuGO_R.html). Unfortunately, you are not explaining what exactly the 
> problems are that you encounter? Can you please explain to me what you are 
> trying to do and in what kind of problems you run? I'll try to give you a 
> hand then.
>
> Regards,
>
> Philip de Groot
> Wageningen University
>
>
> 2013/11/1 >
>
>>  Hello,
>>  
>>  
>> To analyze Human Gene 1.1 st array, I used these CDF files, which 
>> are: HuGene-1_1-st-v1_ascii.CDF (from affymetrix) and (ii) 
>> HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.cdf (from *
>> http://nmg-r.bioinformatics.nl/NuGO_R.html*
>> ).  Unfortunately, I am getting errors that stop me to move forward in 
>> my work.  Please let me know if there is another website to download this 
>> CDF file.
>>
>> Thanks,
>>
>> Jerry  
>>
>> -- 
>> -- 
>> When reporting problems on aroma.affymetrix, make sure 1) to run the 
>> latest version of the package, 2) to report the output of sessionInfo() and 
>> traceback(), and 3) to post a complete code example.
>>  
>>  
>> You received this message because you are subscribed to the Google Groups 
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to 
>> aroma-af...@googlegroups.com
>> To unsubscribe and other options, go to 
>> http://www.aroma-project.org/forum/
>>  
>> --- 
>> You received this message because you are subscribed to the Google Groups 
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>>
>
>

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version of the package, 2) to report the output of sessionInfo() and 
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Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array

2013-11-01 Thread Philip de Groot 
Hi Jerry,

I read your message regarding the binary CDF that you downloaded from
NuGO_R.html (I am responsible for these packages and I am the maintainer of
NuGO_R.html). Unfortunately, you are not explaining what exactly the
problems are that you encounter? Can you please explain to me what you are
trying to do and in what kind of problems you run? I'll try to give you a
hand then.

Regards,

Philip de Groot
Wageningen University


2013/11/1 

> Hello,
>
>
> To analyze Human Gene 1.1 st array, I used these CDF files, which
> are: HuGene-1_1-st-v1_ascii.CDF (from affymetrix) and (ii)
> HuGene-1_1-st-v1,byTranscript-fsetid,pd.hugene.1.1.st.v1.cdf (from *
> http://nmg-r.bioinformatics.nl/NuGO_R.html*
> ).  Unfortunately, I am getting errors that stop me to move forward in my
> work.  Please let me know if there is another website to download this CDF
> file.
>
> Thanks,
>
> Jerry
>
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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