I have normalized data from 60 arays(each array contains 26000 genes). I have done fold change and ANOVA2 analysis in R manually. Now I am left with file containing gene ids, ANOVA P values and respective fold change values (log2 ratios). Will it be possible to load this file to MeV and do clustering based on fold change values (log2 ratios) ?
Regards,
Pankaj Barah
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Sure you can. Just create a *tab* delimited file with gene ids and log2 values in Excel or something you are familiar with.
If the gene ids are not unique it might be useful to add a column at the beginning of the as numeric index (1,2,3 ..n) just as a unique id for each row. The format would like :
UID tab GENE_ID tab SAMPLE_1 tab SAMPLE_2 tab …….SAMPLE_n
In MeV select the default loader (Tab delimited multiple sample files). Remember to UN-Check the Load Annotation box.
Just remember that since there won't be any annotation some of the modules will not work with your data. But clustering modules should be fine.
Best,
Raktim
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I have normalized data from 60 arays(each array contains 26000 genes). I have done fold change and ANOVA2 analysis in R manually. Now I am left with file containing gene ids, ANOVA P values and respective fold change values (log2 ratios). Will it be possible to load this file to MeV and do clustering based on fold change values (log2 ratios) ?
Regards,
Pankaj Barah
Hello,
Sure you can. Just create a *tab* delimited file with gene ids and log2 values in Excel or something you are familiar with.
If the gene ids are not unique it might be useful to add a column at the beginning of the as numeric index (1,2,3 ..n) just as a unique id for each row. The format would like :
UID tab GENE_ID tab SAMPLE_1 tab SAMPLE_2 tab …….SAMPLE_n
In MeV select the default loader (Tab delimited multiple sample files). Remember to UN-Check the Load Annotation box.
Just remember that since there won't be any annotation some of the modules will not work with your data. But clustering modules should be fine.
Best,
Raktim