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.
