Hi Allen,

I am not sure how you produced these files.  My feeling is that you did not
fill in the sample information file correctly.
The process of producing GEO submission file is still not so automatic.
Function “produceGEOSampleInfoTemplate” can help you produce a template of
sample information, but you have to manually modify some information and
fill in the blanks.
Also, you need to check the following website for some information of SOFT
format when you fill in the table:
  http://www.ncbi.nlm.nih.gov/projects/geo/info/soft2.html

As for the platform, we recommend to pick one from the existing platforms if
it is already exists. You can find the existing platform from GEO website.
And fill the platform ID in the sample information table.
After you produced the submission file, you just need to submit
GEOSubmissionFile.txt and supplementaryData.Rdata (optional) files.

We have  submitted quite a few batches of data using them, but bugs might
still exist. Tell me there is still other problems.


Pan



On 2/26/09 11:30 AM, "ss" <affysnp@gmail.com> wrote:

> Dear Pan
> 
> I have been able to use lumi to generate the following
> four files related to GEO submission:
> 
> GEOsampleInfo.txt
> GEOPlatformFile.txt
> GEOSubmissionFile.txt
> supplementaryData.Rdata
> 
> 
> I "rar" them into one archive and use the
> GEO Direct Deposit Slip with file format
> as SOFT. 
> 
> However, I got the errors appended at the end.
> I would be very grateful if you could help me
> 
> regarding this matter. We are catching up a deadline
> for a revised manuscript.Thank you very much for your
> support!!!
> 
> Best wishes
>   Allen
> 
> Your file is invalid; therefore, your submission has failed. This submission
> attempt will be ignored by the GEO curation staff.
> 
> Validating GEO1.rar (/netmnt/geo/websub/soft/gzhang_GEO1.rar)
> 
> Error: At line #2, Unexpected line: '^' expected, found 'Rar!'.
> 
> Error: At line #3, Unexpected line: '^' expected, found '=���?��~!�����!'.
> 
> 
> Error: At line #4, Unexpected line: '^' expected, found
> '��\Gɿ�*?�dﱻ�����y����*q�s���5��>���`�?��aS����������?�oG��y]���s��6G
> ���^���c���E��.�׃�R��A����Cݻ~�R�#�Awk�}��/���9����C�f'.
> 
> 
> Error: At line #5, Unexpected line: '^' expected, found
> '0ݻ����ǌ�3���?�����?���7��"l�ڏ\~U �����I��i5��.��^��3}�������'.
> 
> Error: At line #6, Unexpected line: '^' expected, found
> ']��<�J��,^�F)��r.�ڵt5W���0�v�%?c'.
> 
> 
> Error: At line #7, Unexpected line: '^' expected, found
> '���g���]�q՜Z�T�i�azT��׿d�ϼ�B_����|'�bF.8��ƜV�������W.��+{��<vx��
> ���í��N��ۼ��J�P�^0�|"!ǢG���>@���G�?�֣���^����S�Y��/�(�,�<`�U߁E\�z�\��
> r�E^�8�`�pW����}��'.
> 
> 
> Error: At line #8, Unexpected line: '^' expected, found
> '~Yv�@xa�iG�˥��4�Z�_'&#�\r%�h�[��fB��׿���Y��8�ڼ'���1I=����<����7
> �7�*x�yK�\1���/v(u^y��'�Zm�%*m.��U#���0H��͓��-�O�����9)��ո�Ԛߜ84��y(�3�
> f����j�R\A��R��"�-�"/��yC�
> 
> vX��)�G�K�S~�!�[+y藷��;����
> o9�%|@x~9w�0�����_0����Ir�T��Mq�T�-��NW_�&u��+J���Ǚ�*x��4���'.
> 
> Error: At line #9, Unexpected line: '^' expected, found
> '�=���̴�X��N�,[��`q��Ҹ��qo�o�hCJ�_�Ǆf8�2�=�֞F-ݎ�'.
> 
> 
> Error: At line #10, Unexpected line: '^' expected, found
> '�6�x^)�[*;ۋ�^D�/Ք�)��Y�%!'��%�ap��W�X`,�M)����@qzfpڇY�Me�&q#!�h�֢�
> �[�5�4a�+����+|�fM"��p@F�N�!7 ������j�k.�KݜOt'.
> 
> 
> Error: At line #11, Unexpected line: '^' expected, found 's���x��D�T��`'.
> 
> Error: At line #12, Unexpected line: '^' expected, found
> ''&R���}��v�s@����1F=g���6�����Y7=�&�p1�;�κ���~=�Uo�<�%@�g����
> 
> �34�@J���q.k��^�>��&}��-��Nٸ*�v���4���G0U�=G@�ܟ70Q�tzw5���h�ս}��ݎ+p
> ���&�u�����1��I*�'��!�$���W='.
> 
> Error: At line #13, Unexpected line: '^' expected, found '.'.
> 
> 
> Error: At line #14, Unexpected line: '^' expected, found '2%ϗʋ���S�
> �T�b:���gJ�<��ˊƝL��1����Q)�(E��`��2��C
> �Ά͡|f����v�WE����c~��2�N�;��(�!}��8k���������k��G�¾_$�{q^
> 㻎]�eyv��ɓ|��XCr�K��>!�'.
> 
> 
> Error: At line #15, Unexpected line: '^' expected, found 'NNj�#b�
> �vz�/��}�-&�X�W|�;�k;;suU������ȴ'.
> 
> Error: At line #16, Unexpected line: '^' expected, found 'D�c@�G2i�'.
> 
> 
> Error: At line #17, Unexpected line: '^' expected, found
> '����ᯒ�EXi�7^z��dWc�{-uڪ�k�L���1q��zKz�H0����|C�������)������O��*I�U;Ĭ�
> q�Cet'.
> 
> Error: At line #18, Unexpected line: '^' expected, found
> 
> ''�i�g���F�����Q�g�ϥ˂�h�uoW&?&��U,[z����e�(�8�!u�"��m-�@2�ë�*�Q��m�
> �w���l�;��Z��4��L��j&o�U��RE�dd�����R#����t~����vǷaUʽ�����Ɉj'.
> 
> Error: At line #19, Unexpected line: '^' expected, found '!��,$��
> 
> ��O���Ķv���)��
> tc�6��{�=��-_O�k9���I�o"���X:��'�������yΒD�|ɷp�6H����RO��_�O�ζ�2D���tJ{�
> �g
> ��@H4**�e�"�yB�H:�ļ��]�]�ú�_�9��|�¶�F)� M�)Q;�J-�0��'.
> 
> Error: At line #20, Unexpected line: '^' expected, found
> 
> '!��(V���EIsj���&;1�3��K�� t�%"L(�W��3���xsc��(
> f��ɨbm_vk�w�޹�����y%��l_�]f�R|
> r�;��c�l]!�&��qb��d|*l��ּ�έ��2zp�-�cm��[����`M^�Q�[I�
> �^0$&�W�Ѷ��#�m��TP�s�_�Nt�h�Rq>A��J7��P,|�T�w?}����ul��4
> 
> �4��;�P@���,/դ�6����I�p�P��L_F)�5i<�[�ǤQצ��#$�f�ұ�Y|IYpM0VK��5�"%)�2
> ��4��YPo�U�&_���.�@s��%���\eFh��W�*��U�^����U]��S��|�h�"L��$�̻{�_j�&�[
> .�i
> �<a�e��.�����qډh�c���yIg&"U*hP��ݑ�7��mˍ�'.
> 
> 
> Error: At line #21, Unexpected line: '^' expected, found
> '�I�*r��iŨ�t�C[��)����o��1xQ8_��]����CV����y��"j'.
> 
> Error: Maximum message limit exceeded
> 
> Error: No non-empty submittable definitions were found in the
> 
> submission. The submission had 0 empty definitions and 0 references.
> 
> No validation was performed.
> 
> Nothing submitted due to validation errors
> 
> 
> 



------------------------------------------------------
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan (at) northwestern.edu
------------------------------------------------------




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