Question: GEOsubmission help request
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gravatar for Manca Marco PATH
8.3 years ago by
Manca Marco PATH340 wrote:
Dear Alexandre, good morning. It is my first time trying to submit an expression dataset to GEO and, after reading around the web a bit, I have decided to try to approach the task using the tool you have developed for R/Bioconductor. Unfortunately I get stuck somewhere and the message I receive is not enlightening me in any way, thus I hope you might help me. I have all my .CEL files ("ADV1.CEL","ADV2.CEL","ADV3.CEL","ADV4.CEL", "ADV5.CEL","ADV6.CEL","ADV7.CEL","ADV8.CEL","ADV9.CEL","ADV10.CEL","AD V11.CEL","ADV12.CEL","ADV13.CEL","ADV14.CEL","ADV15.CEL","ADV16.CEL"," EAR1.CEL","EAR2.CEL","EAR3.CEL","EAR4.CEL","EAR5.CEL","EAR6.CEL","EAR7 .CEL","EAR8.CEL","EAR9.CEL","EAR10.CEL","EAR11.CEL","EAR12.CEL","EAR13 .CEL") in the working directory, and I have prepared the sampleInfo.txt and seriesInfo.txt according to the instruction that you offer in your synthetic guide and saved them in the same directory. Nevertheless, when I give the command: > microarray2soft(c("1","2","3","4","5","6","7","8","9","10","11","12" ,"13","14","15","16","17","18","19","20","21","22","23","24","25","26" ,"27","28","29"), "sampleInfo.txt", EarlyAdvancedATHERO,"seriesInfo.txt",softname = "AdvEar.soft", expressionmatrix = "expressionNormalized.txt") the system is reacting like this: Loading sampleinfo... Error in microarray2soft(c("1", "2", "3", "4", "5", "6", "7", "8", "9", : Non-existing raw data files: I have tried uploading the dataset into a affybatch object named like the seriesName, but it doesn't look like it would be making any difference. Where is microarray2soft looking for the raw data? What am I doing wrong? Thank you in advance for your attention and support. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confide...{{dropped:15}}
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ADD COMMENTlink modified 8.3 years ago by Alexandre Kuhn20 • written 8.3 years ago by Manca Marco PATH340
Answer: GEOsubmission help request
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gravatar for Alexandre Kuhn
8.3 years ago by
Alexandre Kuhn20 wrote:
Hi Marco, you might be missing double quotes around EarlyAdvancedATHERO in this command: > microarray2soft(mysampleID, "sampleInfo.txt", EarlyAdvancedATHERO,"seriesInfo.txt",softname = "AdvEar.soft", expressionmatrix = "EarlyAdvancedATHERO.txt") microarray2soft expect a character vector or a character string as the third argument (seriesnames) Alternatively, did you define the variable EarlyAdvancedATHERO to contain the character string "EarlyAdvancedATHERO", with e.g. EarlyAdvancedATHERO<-"EarlyAdvancedATHERO" in which case you could pass the variable EarlyAdvancedATHERO (i.e. without adding quotes). Best wishes, Alexandre --------------------------------------- Dearest Alexandre, I have just now noticed that your email contact has been changed on the Bioconductor page (on the .pdf it's still appearing the old one), thus I retry contacting you for help. As I mention in my previous email attached below I have all my .CEL files in the working directory. After loading GEOsubmission I digit the command: > mysampleID<-c("ADV1.CEL","ADV2.CEL","ADV3.CEL","ADV4.CEL","ADV5.CEL"," ADV6.CEL","ADV7.CEL","ADV8.CEL","ADV9.CEL","ADV10.CEL","ADV11.CEL","AD V12.CEL","ADV13.CEL","ADV14.CEL","ADV15.CEL","ADV16.CEL","EAR1.CEL","E AR2.CEL","EAR3.CEL","EAR4.CEL","EAR5.CEL","EAR6.CEL","EAR7.CEL","EAR8. CEL","EAR9.CEL","EAR10.CEL","EAR11.CEL","EAR12.CEL","EAR13.CEL") > microarray2soft(mysampleID, "sampleInfo.txt", EarlyAdvancedATHERO,"seriesInfo.txt",softname = "AdvEar.soft", expressionmatrix = "EarlyAdvancedATHERO.txt") (I have discovered and solved the previous "naming" inconsistency, somehow) but R pushes out the following: Loading sampleinfo... Loading seriesinfo... Error in microarray2soft(mysampleID, "sampleInfo.txt", EarlyAdvancedATHERO, : One or more series names absent from seriesinfo I am attaching my sampleInfo.txt and my seriesInfo.txt for you to be able to check, might you want to. I am now completely lost, sincerely. Could you tell me where I am wrong? Thank you in advance. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca@maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: Manca Marco (PATH) Inviato: giovedì 21 aprile 2011 10.55 A: kuhnam@mail.nih.gov; bioconductor mailing list Oggetto: GEOsubmission help request Dear Alexandre, good morning. It is my first time trying to submit an expression dataset to GEO and, after reading around the web a bit, I have decided to try to approach the task using the tool you have developed for R/Bioconductor. Unfortunately I get stuck somewhere and the message I receive is not enlightening me in any way, thus I hope you might help me. I have all my .CEL files ("ADV1.CEL","ADV2.CEL","ADV3.CEL","ADV4.CEL","ADV5.CEL","ADV6.CEL","AD V7.CEL","ADV8.CEL","ADV9.CEL","ADV10.CEL","ADV11.CEL","ADV12.CEL","ADV 13.CEL","ADV14.CEL","ADV15.CEL","ADV16.CEL","EAR1.CEL","EAR2.CEL","EAR 3.CEL","EAR4.CEL","EAR5.CEL","EAR6.CEL","EAR7.CEL","EAR8.CEL","EAR9.CE L","EAR10.CEL","EAR11.CEL","EAR12.CEL","EAR13.CEL") in the working directory, and I have prepared the sampleInfo.txt and seriesInfo.txt according to the instruction that you offer in your synthetic guide and saved them in the same directory. Nevertheless, when I give the command: > microarray2soft(c("1","2","3","4","5","6","7","8","9","10","11","12"," 13","14","15","16","17","18","19","20","21","22","23","24","25","26"," 27","28","29"), "sampleInfo.txt", EarlyAdvancedATHERO,"seriesInfo.txt",softname = "AdvEar.soft", expressionmatrix = "expressionNormalized.txt") the system is reacting like this: Loading sampleinfo... Error in microarray2soft(c("1", "2", "3", "4", "5", "6", "7", "8", "9", : Non-existing raw data files: I have tried uploading the dataset into a affybatch object named like the seriesName, but it doesn't look like it would be making any difference. Where is microarray2soft looking for the raw data? What am I doing wrong? Thank you in advance for your attention and support. Best regards, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca@maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** [[alternative HTML version deleted]]
ADD COMMENTlink written 8.3 years ago by Alexandre Kuhn20
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