Question: Deseq2 RIP seq analisys
1
gravatar for Joan Gibert
16 months ago by
Joan Gibert20
Barcelona/PRBB
Joan Gibert20 wrote:

I am following this: https://support.bioconductor.org/p/61509/

After HTseq, Deseq2 cannot perform the (IP for B / IP for A) / (Input for B / Input for A). I did this by adding two different "Factors". The first with the RIPseq data (1st Factor level WT; 2nd Factor level KO) and the second the RNAseq data (1st Factor level WT; 2nd Factor level KO).

It gives the following error:

Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Error in row.names<-.data.frame(*tmp*, value = value) :

I google it and it seems that it's something regarding with the input names. I changed them but still the same.

What do you think guys that I am doing wrong?

Thanks! Joan

deseq2 • 522 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson23k • written 16 months ago by Joan Gibert20
1

Here it is the full error:

Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Error in row.names<-.data.frame(*tmp*, value = value) : duplicate 'row.names' are not allowed Calls: rownames<- ... rownames<- -> row.names<- -> row.names<-.data.frame Warning message: non-unique values when setting 'row.names':

ADD REPLYlink written 16 months ago by Joan Gibert20

Hello - Are you performing the analysis within Galaxy? If so, where? Galaxy Main http://usegalaxy,org, a local, a cloud, or some other public server (URL)?

ADD REPLYlink written 16 months ago by Jennifer Hillman Jackson23k

Hi! I'm using the Galaxy Main http://usegalaxy,org

ADD REPLYlink written 16 months ago by Joan Gibert20
0
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello -

While the error message indicates that there are duplicates within the input, a google on this error message reveals that it is commonly associated with a missing tool dependency. If true, that is something that would need to be fixed either with the wrapped tool itself or on the http://usegalaxy.org server.

Would you please send in a bug report from one of the error datasets for us to look at? Please make sure all inputs and the job itself are undeleted. Please include a link to this Biostars post in the comments so we can link the two.

How to send in a bug from Galaxy Main: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks for reporting the problem, Jen, Galaxy team

ADD COMMENTlink modified 16 months ago • written 16 months ago by Jennifer Hillman Jackson23k
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