--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-dis...@googlegroups.com.
To post to this group, send email to wikipathwa...@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
Hi Petar,Can you send a few rows of your input file?Thanks,
Kristina
On Dec 5, 2017, at 4:37 AM, Petar Donchev <donc...@gmail.com> wrote:
Dear All,I am having issue with data import from Illumina microarray analysis. The data is preprocessed file containing the ID of the probes (numerical) and ILMN_ identifier, as well as normalised expression values and FoldChange information (comparison between control and sample).I have saved the file as text (tab delimited) but the import step gives me information that all of the imput lines are ecceptions and and the end the window says that I have all 48102 lines unrecognized.I have tried several times using different options without any success. The gene list from Hs_Derby_ensemble has been loaded in the program prior to the samples sheet.The version of the chip I have used for the microarray analysis is Human ht-12_v4_0_r2_15002873_b.I hope somebodfy can lifet me up from this situation.Regards
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Dear Hristina,Thank you for reply.Please, find attached an example sheet of my data with the respective accession names (ILMN_; 10008 ...)Kind regards,Petar
2017-12-06 21:02 GMT+02:00 Kristina Hanspers <kristina.hanspers@gladstone.ucsf.edu>:
Hi Petar,Can you send a few rows of your input file?Thanks,
Kristina
On Dec 5, 2017, at 4:37 AM, Petar Donchev <donc...@gmail.com> wrote:
Dear All,I am having issue with data import from Illumina microarray analysis. The data is preprocessed file containing the ID of the probes (numerical) and ILMN_ identifier, as well as normalised expression values and FoldChange information (comparison between control and sample).I have saved the file as text (tab delimited) but the import step gives me information that all of the imput lines are ecceptions and and the end the window says that I have all 48102 lines unrecognized.I have tried several times using different options without any success. The gene list from Hs_Derby_ensemble has been loaded in the program prior to the samples sheet.The version of the chip I have used for the microarray analysis is Human ht-12_v4_0_r2_15002873_b.I hope somebodfy can lifet me up from this situation.Regards
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsubscrib...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsubscrib...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
-----------------------------------------------
Martina Summer-Kutmon, PhD
email: mku...@gmail.com
skype: mkutmon
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-dis...@googlegroups.com.
To post to this group, send email to wikipathwa...@googlegroups.com.
Hi Petar,In my test, 4 out of the 8 example probes you sent import. The rest are not recognized by our database, which is built based on Ensembl. Its possible Ensembl did not include these probes for some reason.Regards,Kristina
On Dec 7, 2017, at 4:48 AM, Petar Donchev <donc...@gmail.com> wrote:
Dear Martina,I tried with this column, but unfortunately on my side there is some problem.As the matter of fact I am using a simplified version of the example I sent you, which contains less number of columns. But the accession data is same and the expression values together with the fold change.I will give it a try and will come back to you with response whether it works or not.Thank you for your support.petar
Kristina
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
-----------------------------------------------
Martina Summer-Kutmon, PhD
email: mku...@gmail.com
skype: mkutmon
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
Dear Tina,That is correct.I am having 48105 lines (genes) and more than 11 000 unrecognized genes. Nevertheless there are 'empty' line in the data - some sort of controls for negative background which cannot be uploaded in PathVisio. The rest are the 'unstable" accessions that change from version to version and are not very specific because some genes are not very well described. These genes are given names like e.g. LOC14234. They are not important for me.However I am getting the following message whenever I am trying to select a particular pathway from the 'Search' tab on the right:Error message:class java.lang.reflect.InvocationTargetException: nullSee error log for detailsclass org.pathvisio.core.model.ConverterExceptionHave you any idea why this message appears?KInd regards,Petar
Kristina
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
-----------------------------------------------
Martina Summer-Kutmon, PhD
email: mku...@gmail.com
skype: mkutmon
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "wikipathways-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsubscr...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsubscrib...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsubscrib...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
--
-----------------------------------------------
Martina Summer-Kutmon, PhD
email: mku...@gmail.com
skype: mkutmon
--
You received this message because you are subscribed to a topic in the Google Groups "wikipathways-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/wikipathways-discuss/HZo62y10SUw/unsubscribe.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To unsubscribe from this group and stop receiving emails from it, send an email to wikipathways-discuss+unsub...@googlegroups.com.
To post to this group, send email to wikipathways-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/wikipathways-discuss.
For more options, visit https://groups.google.com/d/optout.
To unsubscribe from this group and all its topics, send an email to wikipathways-discuss+unsub...@googlegroups.com.