Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array
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, ndig...@gmail.com javascript: 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 aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-af...@googlegroups.comjavascript: 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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetr...@googlegroups.com javascript:. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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-affymetrix@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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array
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 -- -- 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-affymetrix@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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array
On Sat, Nov 2, 2013 at 10:48 AM, jerrych...@gmail.com 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 jerry...@gmail.com 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
Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array
On Sat, Jan 11, 2014 at 4:59 AM, ndigi...@gmail.com 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 aroma.affymetrix group with website http://www.aroma-project.org/. 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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-affymetrix@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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
Re: [aroma.affymetrix] CDF file for Human Gene 1.1 st array
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 javascript: [jerry...@gmail.com javascript:] Sent: Saturday, November 02, 2013 12:29 AM To: aroma-af...@googlegroups.com javascript: Cc: jerry...@gmail.com javascript:; 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 jerry...@gmail.com 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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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-affymetrix@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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
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 jerry...@gmail.com javascript: 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*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.comjavascript: 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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetr...@googlegroups.com javascript:. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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-affymetrix@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 aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
