Galaxy to Cummerbund Data Import Issue

[mclo41]

Hi,

I am having issues importing my cuffdiff data (generated through Galaxy) into cummerbund. When using R3.1.1 and cummerbund2.7.2 (or 2.6.1) I get the following warning and some processes (like dispersion plot) do not work:

Warning messages:
1: attributes are not identical across measure variables; they will be dropped

When trying to make a dispersion plot in v.2.7.2....
Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
replacement has 1 row, data has 0

This issue is resolved if I use cummerbund 1.2.0, but I would like to use the latest version of cummerbund to take advantage of newer plotting functions, like dispersion plot and PCA.

Can anyone give me advice as to what this issue is and how it can be resolved?

Thanks!

[jp.]

I got the same error :
Warning messages:
1: attributes are not identical across measure variables; they will be dropped

Did you get any solution?? please let me know...
Second thing, I think its not an error, its just warning message so we can just ignore them and go on ....
anybody has idea ?

Hi,

I am having issues importing my cuffdiff data (generated through Galaxy) into cummerbund. When using R3.1.1 and cummerbund2.7.2 (or 2.6.1) I get the following warning and some processes (like dispersion plot) do not work:

Warning messages:
1: attributes are not identical across measure variables; they will be dropped

When trying to make a dispersion plot in v.2.7.2....
Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
replacement has 1 row, data has 0

This issue is resolved if I use cummerbund 1.2.0, but I would like to use the latest version of cummerbund to take advantage of newer plotting functions, like dispersion plot and PCA.

Can anyone give me advice as to what this issue is and how it can be resolved?

Thanks!

[mclo41]

Hi JP,

Turns out that warning message is something that can be ignored. The error message is a result of Galaxy output not being entirely compatible with cummeRbund. To resolve this issue, run the cufflinks pipeline via command line.

[jp.]

Thank you mclo41
Yes, I did compete my run using command lines on my server and these were just warnings on cummRbunds, So, I just ignored then because there were not errors....
Thank you again
jp

Hi JP,

Turns out that warning message is something that can be ignored. The error message is a result of Galaxy output not being entirely compatible with cummeRbund. To resolve this issue, run the cufflinks pipeline via command line.

[Neberir]

Hi,

I ran the cufflinks pipeline by using command line, but still facing the same problem.

Could some tell me how to solve this issue?

Thanks

Hi JP,

Turns out that warning message is something that can be ignored. The error message is a result of Galaxy output not being entirely compatible with cummeRbund. To resolve this issue, run the cufflinks pipeline via command line.

[Zapages]

Please check my answer out on Iplant regards to importing Cuffdiff2 data: http://ask.iplantcollaborative.org/q...-gff3gtf-file/

I hope this helps a bit.

-Zapages