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Question: Issues uploading database for metabolomic data analysis with Pathway Activity Profiling - PAPi
1
gravatar for hp71727
19 months ago by
hp7172710
The Pennsylvania State University, University Park, PA
hp7172710 wrote:

Hello all,

I am trying to analyze a plant metabolomics database with PAPi, but haven't been able to get even started as there is a constant error apparently related with the data formatting. All examples from the package work fine, and my own data looks in the same format as the example metabolomics data set. My database contains 20 compounds (rows) and 80 samples (columns), the column names are "Sample1", "Sample2" ... "Sample80"; the second row indicate two conditions, healthy or infected. The first column has the KEGG codes instead of compound names. Below is a portion of my database (first six rows and columns).

> papivoc[1:6, 1:6]
       Names   Sample1   Sample2   Sample3   Sample4   Sample5
1 Replicates   healthy   healthy   healthy   healthy   healthy
2     C19757 2.1927358 1.6329086 2.4302252 0.5544893      <NA>
3     C00042      <NA> 1.0817259      <NA>      <NA> 0.7601545
4     C11391      <NA> 0.9295942      <NA>      <NA>      <NA>
5     C14272 1.2880552 1.2894686 0.8696715 1.9424637      <NA>
6     C07287 1.4880006 1.4538546 1.2594548 1.2812344 0.2241397

All the columns in the data.frame are formatted as characters

> str(papivoc)
'data.frame':    21 obs. of  81 variables:
 $ Names   : chr  "Replicates" "C19757" "C00042" "C11391" ...
 $ Sample1 : chr  "healthy" "2.1927358" NA NA ...
 $ Sample2 : chr  "healthy" "1.6329086" "1.0817259" "0.9295942" ...
 $ Sample3 : chr  "healthy" "2.4302252" NA NA ...

The error message is the following

> papiresults <- papi(papivoc, save = FALSE, offline = FALSE)
[1] "Online analysis being performed..."
[1] "PAPi in progess..."
[1] "Data frame loaded..."
  |=                                                 |   2%
Error in names(comp)[1] <- "value" : 
  'names' attribute [1] must be the same length as the vector [0]
In addition: Warning message:
In if (getpath != 0) { :
  the condition has length > 1 and only the first element will be used

 

Thanks for any help in advance

 

Hannier Pulido

Graduate student

Department of Biology, Penn State University

ADD COMMENTlink modified 8 months ago by k_hulce10 • written 19 months ago by hp7172710
2
gravatar for Raphael Aggio
19 months ago by
Raphael Aggio30 wrote:

Hi Hannier,

I have tested PAPi and it seems to b working well.

Would you be able to send me your dataset in a csv file so I can test it?

Cheers.

Raphael

ADD COMMENTlink written 19 months ago by Raphael Aggio30

Hi Raphael, 

Sorry for the delay in my answer.

Yes, I can send along the csv file. I uploaded it to my github account:

https://github.com/hannierpulido/database-for-PAPi.git

Thanks in advance.

Best,

Hannier

ADD REPLYlink written 18 months ago by hp7172710
1
gravatar for k_hulce
8 months ago by
k_hulce10
k_hulce10 wrote:

I am having the same issue;  how did you fix this?  Is there an update I need to do?  

Thanks in advance,

Kara

ADD COMMENTlink written 8 months ago by k_hulce10

typically when confronted with this type of problem I subset the data to a few rows (or 1) and go from there. also, i explicitly type/cast the data as a string no matter what is reported by str().

ADD REPLYlink written 8 months ago by rreck0

Thanks, I'll give this a try. 

ADD REPLYlink written 8 months ago by k_hulce10
0
gravatar for Raphael Aggio
19 months ago by
Raphael Aggio30 wrote:

 

Hi Hannier,

I am sorry to hear that you are having problems with PAPi. I will investigate your problem and come back to you soon.

Cheers.

Raphael

ADD COMMENTlink written 19 months ago by Raphael Aggio30

Thanks for getting back to me and please let me know if I can provide you with more information.

 

ADD REPLYlink written 19 months ago by hp7172710
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