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","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")

> 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: giovedė 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","ADV7.CEL","ADV8.CEL","ADV9.CEL","ADV10.CEL","ADV11.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@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]]

