Hi Allen,
By comparing your chip version HumanWG6_V2_11223189_B with the
platform
GPL6790, I found GPL6790 uses âTargetâ Id as identifier. Because
function
produceGEOSubmissionFile assumes âProbeIDâ is used by default, it
causes ID
mismatch errors. As a temporary, you can first convert your data as
âTargetâ
ID indexed, then produce GEO submission file.
Here is some example code:
## suppose lumiRaw is the raw data, lumiNormalized is the normalized
data
and "sampleInfoFile.txt" keeps the sample information
> illuminaID = nuID2IlluminaID(featureNames(lumiRaw), species="Human",
idType="Gene")
> featureNames( lumiRaw) <- featureNames( lumiNormalized ) <-
illuminaID
>
> produceGEOSubmissionFile(lumiNormalized, lumiRaw, sampleInfo =
"sampleInfoFile.txt")
Hope this will work.
Pan
On 2/26/09 1:18 PM, "Sean Davis" <seandavi@gmail.com> wrote:
>
>
> On Thu, Feb 26, 2009 at 1:59 PM, ss <affysnp@gmail.com> wrote:
>> Dear Sean,
>> Â
>> You are absolutely right. ID_REF in my submission file does not
match IDs
>> in GPL6790,
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6790.
>> Â
>> The first two rows in my submission file look like:
>> Â
>> ID_REFÂ nuIDÂ VALUEÂ RAW_VALUEÂ BEAD_STDERRÂ Detection_PvalÂ
Avg_NBEADS
>> 0006960451 NQqs8dKRwVSgI4SRPk 7.67644911129066 81.2483 6.9638Â
0.997088792Â 41
>>
0002850504Â ERVJG9FehRAB6AoIq0Â 6.89318565949701Â 0.3596772Â 2.239353Â
0.5924309Â 4>>
0
>> Â
>> I appreciate your help!
>> Â
>
> I see. So, you have nuID in your data. You can use the
nuID2IlluminaID()
> function in the lumi package to do the mapping from nuID to ILMN
ids, I
> believe. That should fix the problem.
>
> Sean
>
> Â
>> Allen
>>
>> On Thu, Feb 26, 2009 at 1:49 PM, Sean Davis <seandavi@gmail.com>
wrote:
>>>
>>>
>>> On Thu, Feb 26, 2009 at 1:30 PM, ss <affysnp@gmail.com> wrote:
>>>> Hi Pan,
>>>>
>>>> Thanks much! I did manually fill up the blanks in the sampleInfo
otherwise
>>>> GEOSubmissionFile would not be generated. You are right about the
platform
>>>> ID (I picked one, updated the sampleInfo file and submitted the
>>>> GEOSubmissionFile
>>>> again).
>>>>
>>>> Now I got the error as:
>>>>
>>>> Error: At line #27, Invalid ID_REF value "0006960451" in sample
>>>> FOM173-rep1.
>>>> Error: At line #28, Invalid ID_REF value "0002850504" in sample
>>>> FOM173-rep1.
>>>> Error: At line #29, Invalid ID_REF value "0007560397" in sample
>>>> FOM173-rep1.
>>>> Error: At line #30, Invalid ID_REF value "0005360747" in sample
>>>> FOM173-rep1.
>>>> Error: At line #31, Invalid ID_REF value "0002600731" in sample
>>>> FOM173-rep1.
>>>> Error: At line #32, Invalid ID_REF value "0003990110" in sample
>>>> FOM173-rep1.
>>>> Error: At line #33, Invalid ID_REF value "0002120309" in sample
>>>> FOM173-rep1.
>>>> Error: At line #34, Invalid ID_REF value "0006420474" in sample
>>>> FOM173-rep1.
>>>> Error: At line #35, Invalid ID_REF value "0000670095" in sample
>>>> FOM173-rep1.
>>>> Error: At line #36, Invalid ID_REF value "0000130367" in sample
>>>> FOM173-rep1.
>>>> Error: At line #37, Invalid ID_REF value "0003830242" in sample
>>>> FOM173-rep1.
>>>> Error: At line #38, Invalid ID_REF value "0006480041" in sample
>>>> FOM173-rep1.
>>>> Error: At line #39, Invalid ID_REF value "0007510608" in sample
>>>> FOM173-rep1.
>>>> Error: At line #40, Invalid ID_REF value "0001570494" in sample
>>>> FOM173-rep1.
>>>> Error: At line #41, Invalid ID_REF value "0001740092" in sample
>>>> FOM173-rep1.
>>>> Error: At line #42, Invalid ID_REF value "0003440520" in sample
>>>> FOM173-rep1.
>>>> Error: At line #43, Invalid ID_REF value "0006520451" in sample
>>>> FOM173-rep1.
>>>> Error: At line #44, Invalid ID_REF value "0000780746" in sample
>>>> FOM173-rep1.
>>>> Error: At line #45, Invalid ID_REF value "0000150546" in sample
>>>> FOM173-rep1.
>>>> Error: Maximum message limit exceeded
>>>> Your submission has failed MIAME validation.
>>>> Nothing submitted due to validation errors
>>>> Added 0 of 4 entities.
>>>>
>>>> How to fix this? Any suggestions?
>>>
>>> Hi, Allen.
>>>
>>> What do the IDs in the GPL look like? Does your ID_REF match?Â
>>>
>>> I would suggest that you work with the GEO staff to do your
submission as
>>> these are GEO errors. Perhaps you can suggest changes to Pan
after you have
>>> completed the submission and know better where the problems arose.
>>>
>>> Sean
>>> Â
>>>>
>>>>
>>>> On Thu, Feb 26, 2009 at 1:04 PM, Pan Du <dupan@northwestern.edu>
wrote:
>>>>
>>>>> > Hi Allen,
>>>>> >
>>>>> > I am not sure how you produced these files. Â 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 ââ¬ÅproduceGEOSampleInfoTemplateâ⬠ 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:
>>>>> > Â
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:
>>>>> >
>>>>> > Â 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
>>>>> > Â *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
>>>>> > ' ��\ Gÿ
�*?�dﱻ�����
y����*q�s���
>>>>> 5��>�
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>>>>> >
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>>>>> ¿½ï¿½A����Cû ~�R�#�
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>>>>> �C �f'.
>>>>> >
>>>>> >
>>>>> > Error: At line #5, Unexpected line: '^' expected, found
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>>>>> �����I� �i5��.ï¿Â
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>>>>> >
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>>>>> > ��,^�F)��r.�õt5W��Ã
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>>>>
>>>>> >
>>>>> >
>>>>> > Error: At line #7, Unexpected line: '^' expected, found
>>>>> > '���g���]�qÃÅZ�Tï¿
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>>>>> � � �| '�b F.8��ÃÅV��Ã
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>>>>
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>>>>> >
>>>>> > Error: At line #8, Unexpected line: '^' expected, found
>>>>> > '~ Yv�@xa�iïâ½ G��4�Z
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>>>>> *m.� �U#��
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>>>>
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>>>>> > Error: At line #9, Unexpected line: '^' expected, found
>>>>> > '�=���ô�X��N�,[ï¿
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>>>>> hCJ�_�Ãâf8�2�=�ÞF -�'.
>>>>
>>>>> >
>>>>> >
>>>>> > Error: At line #10, Unexpected line: '^' expected, found
>>>>> > ' �6�x^)�ïâ¯[*;Ãâ¹Ã¯Â¿Â½^
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>>>>> ������j�k.� KÃÅOt'.
>>>>> >
>>>>> >
>>>>> > Error: At line #11, Unexpected line: '^' expected, found
>>>>> 's���x��D�T��` '.
>>>>
>>>>> >
>>>>> > Error: At line #12, Unexpected line: '^' expected, found
>>>>> >
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>>>>>
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>>>>> >
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>>>>> !�$�� �W='.
>>>>
>>>>> >
>>>>> > Error: At line #13, Unexpected line: '^' expected, found '.'.
>>>>> >
>>>>> >
>>>>> > Error: At line #14, Unexpected line: '^' expected, found '
>>>>> 2%ÃâÃâ¹Ã¯Â¿Â½Ã¯Â¿Â½Ã¯Â¿Â½S�
>>>>> > �T�b:���g J�<��ÃÅ Ã
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>>>>> >
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>>>>> > Error: At line #15, Unexpected line: '^' expected, found 'N
Nj�#b�
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>>>>> > }�-&� X�W|�;�k;;suU�
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>>>>> >
>>>>> > Error: At line #16, Unexpected line: '^' expected, found
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>>>>
>>>>> >
>>>>> >
>>>>> > Error: At line #17, Unexpected line: '^' expected, found
>>>>> > '�
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>>>>
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>>>>> > Error: At line #18, Unexpected line: '^' expected, found
>>>>> >
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>>>>> �|�ö�F) � M�) Q;
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>>>>
>>>>> >
>>>>> > Error: At line #20, Unexpected line: '^' expected, found
>>>>> >
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&;1�3�� K�� t�%"L(
>>>>> �W��3���xs c� �(
>>>>> > f��èbm_vk�w�ù���ï¿Â
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>>>>> > r�;�
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>>>>> �ü�ÃÂ��2zp�-�
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>>>>> > � ^0 $&�W�ö��
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>>>>> A��J7��P,|�T�w? }
��� �ul��4
>>>>> >
>>>>> > �4��;�P@� ��,
/ä�6��� �I�p�P� �L_
>>>>> F)�5i<�[�äQæ��#$
�f�Ã񋨫Y|I YpM 0
>>>>> > VK��5�"%)�2��4
��YPo�U�&_
>>>>> ���.�@s��%���\
>>>>> eFh��W�*��U�^���ïÂ
¿Â½U]��S��|� h�"L��
>>>>> > $�û{�_j� &�[.�i
>>>>> > �<a�e��.�����q Ãâ°h�c���="" yi="" g&"u*hp�="">>>>> �Ãâ�7��mà �'.
>>>>> >
>>>>> >
>>>>> > Error: At line #21, Unexpected line: '^' expected, found
'�I�*r�
>>>>> �iÃ
¨ï¿½t
>>>>> >
�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 Â 60611
>>>>> > Office (312) 503-2360; Fax: (312) 503-5388
>>>>> > dupan (at) northwestern.edu <http: northwestern.edu=""/>
>>>>> > ------------------------------------------------------
>>>>> >
>>>>> >
>>>>> >
>>>>
>>>> Â Â Â Â [[alternative HTML version deleted]]
>>>>
>>>>
>>>> _______________________________________________
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>>>> Bioconductor@stat.math.ethz.ch
>>>>
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>>>> Search the archives:
>>>>
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>>>
>>
>
>
------------------------------------------------------
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
------------------------------------------------------
[[alternative HTML version deleted]]
