# Struggling with the input datasets

**URL:** <https://forum.biobakery.org/t/struggling-with-the-input-datasets/2514>\
**Category:** CCREPE\
**Created:** [August 27, 2021, 2:06pm UTC](https://forum.biobakery.org/t/struggling-with-the-input-datasets/2514 "2021-08-27T14:06:59Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![miguensblanco](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/miguensblanco/32/456_2.png) [@miguensblanco](https://forum.biobakery.org/u/miguensblanco)\
**Post date:** [August 27, 2021, 2:07pm UTC](https://forum.biobakery.org/t/struggling-with-the-input-datasets/2514/1 "2021-08-27T14:07:00Z")

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Hi guys,

Thanks for this very great tool.

I have been trying to upload my dataset and recurrently, I have been getting the following error when trying to run the command:

> ccrepe.results \<-ccrepe(x = otuY, iterations = 20, min.subj = 10, make.output.table = TRUE)

:

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/a73b0ead529e7b239a7a14980cc32fa78db1c678.png)

I produced my dataset from a phyloseq object and I have tried many ways to upload it and formatted it following the tutorial, however I always get the “$ operator error”

That’s how my dataset looks like

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/1X/edbcd9747021e5463d096f5c5299e1a65f95b429.png)

I have been formatting data sets for a day and a half to the border of paranoia, so any tip will be really appreciate 🙂

Thanks,

Jesus

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<div class="post-metadata">

**Author:** ![Kelsey\_Thompson](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kelsey_thompson/32/65_2.png) [@Kelsey\_Thompson](https://forum.biobakery.org/u/Kelsey_Thompson)\
**Post date:** [September 2, 2021, 2:03pm UTC](https://forum.biobakery.org/t/struggling-with-the-input-datasets/2514/2 "2021-09-02T14:03:17Z")

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Hi Jesus (@miguensblanco),

Sorry, you are running into issues! This one is going to be hard to diagnosis without a minimally reproducible example. Are you able to send some data (either through here or via email)? It can be either your real data, a toy example, or a blinded version.

Best,  
Kelsey

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<div class="post-metadata">

**Author:** ![miguensblanco](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/miguensblanco/32/456_2.png) [@miguensblanco](https://forum.biobakery.org/u/miguensblanco)\
**Post date:** [September 2, 2021, 5:45pm UTC](https://forum.biobakery.org/t/struggling-with-the-input-datasets/2514/3 "2021-09-02T17:45:14Z")

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[otuY.csv](https://forum.biobakery.org/uploads/short-url/pIMI2IzqDvk0ktJVyEirqzsNi40.csv) (17.7 KB)  
[otuY.txt](https://forum.biobakery.org/uploads/short-url/sS3dG2XBaHc946LaRkx0jg7lX3b.txt) (62.5 KB)

Hi Kesley,

Thanks for the prompt reply!!

I was not sure if it was allowed to upload my files! I just uploaded one dataset formatted in two different ways, hopefully it makes sense.

The data came from a phyloseq object which after some filters for the taxa abundance was cluster to the genus level using the command _tax\_glom_. Finally I save the otu table as csv file (write.csv) (or as a txt for the second dataset) and then import the dataset back to R as a dataframe.

If it is not enough I am happy to send my script or whatever is needed!

Thanks again,

Jesus

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<div class="post-metadata">

**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [September 6, 2021, 3:29pm UTC](https://forum.biobakery.org/t/struggling-with-the-input-datasets/2514/4 "2021-09-06T15:29:13Z")

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I’m not exactly sure where the issue is coming from, but I was able to get results with the following code.

```auto
library(ccrepe)

otuY = read.table("C:/Users/aghazi/Downloads/otuY.csv",
                  sep = ",",
                  header = TRUE)

otuY$X = NULL # Delete the sample IDs

ccrepe(x = otuY, iterations = 20, min.subj = 10, make.output.table = TRUE)

```

I also tried starting from your .txt file (which didn’t have sample IDs) and was also able to get results.