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 <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.
