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The following warning messages when trying Circ.test() with the processed Westholm et al. data from CircTest package appears 10x.

Warning messages:
1: In betabin(cbind(circ, tot - circ) ~ group, ~1, data = testdat) : 
Possible convergence problem. Optimization process code: 10 (see ?optim).

Dear Tobias,

please add circular over total count ration to spreadsheet output.

Hi,

I have installed the CircTest (0.1.1) package with aod (1.3.1) today. I followed all the filtering steps with no apparent problems. Here's the Circ.filter parameters used:

Circ_filtered <- Circ.filter(circ = CircRNACount,
linear = LinearCount,
Nreplicates = 3,
filter.sample = 3,
filter.count = 5,
percentage = 0.1
)

Got the LinearCount_filtered as said in the documentation.

I wanted to compare two conditions, each with three replicates. Then I used Circ.test(...) as below:
test <- Circ.test(Circ_filtered, Linear_filtered, group=c(rep(1,3),rep(2,3)))

The CircTest gave me a hard time. There were a ton of "Possible convergence problem" messages.

Loading required package: aod

Possible convergence problem. Optimization process code: 10 (see ?optim).

Possible convergence problem. Optimization process code: 10 (see ?optim).
...

What might went wrong?

Any help is appreciated.

Eric.

stop output from being displayed

> library(CircTest)
> data(Circ)
> CircRNACount_filtered <- Circ
> data(Coordinates)
> CircCoordinates_filtered <- Coordinates
> data(Linear)
> LinearCount_filtered <- Linear
> test<-Circ.test(CircRNACount_filtered,LinearCount_filtered,CircCoordinates_filtered,group=c(rep(1,6),rep(2,6),rep(3,6)))
[1] 0.02014347
[1] 0.6495478
[1] 8.456228e-06
[1] 0.1486048
[1] 0.0002517429
[1] 0.8817177
[1] 0.2396249
[1] 0.0001037317
[1] 0.0003191368
[1] 0.0003216454
[1] 6.836387e-10
[1] 1.672421e-06
[1] 0.7849758
[1] 0.0160119
[1] 0.489192
[1] 1.468186e-05
[1] 0.03070399
[1] 3.847381e-10
[1] 0.02676743
[1] 4.209558e-06
[1] 0.5967388
[1] 0.02568653
[1] 0.02393622
[1] 0.3644774
[1] 0.7463216
[1] 0.06449776
[1] 5.429645e-05
[1] 4.048711e-06
[1] 0.03379427
[1] 0.3265092
[1] 0.002235983
[1] 0.2274599
[1] 0.009610914
[1] 0.4899821
[1] 0.0006485977
[1] 0.5124443
[1] 0.04395746
[1] 0.8994835
[1] 0.0001100703
[1] 0.02784646
[1] 9.799968e-07
[1] 0.7975485
[1] 0.0007054044
[1] 0.0001130478
[1] 5.183719e-05
[1] 0.01393172
[1] 0.05496929
[1] 0.6700679
[1] 0.1896846
[1] 0.2348698
[1] 0.8231842
[1] 0.008174306
[1] 3.229639e-13
[1] 0.711166
[1] 0.04607245
[1] 9.197512e-05
[1] 0.001747302
[1] 0.001515325
[1] 5.394975e-06
[1] 0.001673671
[1] 7.81371e-05
[1] 0.7907509
[1] 4.895354e-05
[1] 0.02176042
[1] 4.665157e-13
[1] 0.06752149
[1] 0.4165374
[1] 5.141057e-08
[1] 0.01016052
[1] 0.01168991
[1] 0.004350761
[1] 0.000183985
[1] 1.307679e-07
[1] 0.7880073
[1] 8.292977e-06
[1] 0.000164235
[1] 5.441918e-05
[1] 6.546695e-06
[1] 0.4178892
[1] 5.66796e-06
[1] 0.239462
[1] 0.5554723
[1] 0.001377761
[1] 0.05156439
[1] 0.9397476
[1] 0.0001007124
[1] 0.1373332
[1] 0.001412486
[1] 0.005676716
[1] 1.150676e-05
[1] 0.0009736881
[1] 1.625895e-05
[1] 5.320809e-09
[1] 0.0001483919
[1] 0.8086524
[1] 0.006413823
[1] 0.2311123
[1] 0.602383
[1] 0.000211141
[1] 0.002293403
[1] 0.001499613
[1] 2.55947e-05
[1] 6.48444e-07
[1] 0.07887855
[1] 0.4706678
[1] 0.0003701373
[1] 2.536641e-06
[1] 1.605286e-06
[1] 0.0001751859
[1] 0.02394134
[1] 0.04379356
[1] 0.0904197
[1] 0.8985729
[1] 0.003101775
[1] 0.03430905
[1] 0.006915007

test=Circ.test(CircRNACount_filtered,LinearCount_filtered,CircCoordinates_filtered,group=annot)
Fehler in fitAlt@param[2][["group2"]] : Indizierung ausserhalb der Grenzen

group2 seems to be hard coded

annot
[1] "SCRG" "SCRG_+Hypoxia_24h" "siADAR1_Hypoxia_24h"
[4] "siADAR2_Hypoxia_24h" "siADAR12_+Hypoxia_24h" "SCRG"
[7] "SCRG_+Hypoxia_24h" "siADAR1_Hypoxia_24h" "siADAR2_Hypoxia_24h"
[10] "siADAR12_+Hypoxia_24h" "SCRG" "SCRG_+Hypoxia_24h"
[13] "siADAR1_Hypoxia_24h" "siADAR2_Hypoxia_24h" "siADAR12_+Hypoxia_24h"

See thread of circtools issue #5 for details

I noticed that when I input the results from DCC it says that the number of columns aren't the same since the CircRNACounts file has an extra column for strandedness. I don't see this addressed in the documentation, but I fixed this by setting the strands column to NULL. Also, I don't see an explanation of circle_description = 1 arguement, which in the case of DCC should just be left at its default number.

The plots generated have the x label "groupindicator1" which isnt very visually appealing or publication quality.

This can be improved by adding " xlab("Condition") +" to line 109 of Circ.lineplot.R

Dear Sir or Madam,

I have finished to do circRNA calling by DCC and is trying to use CircTest to perform circRNA filtering.

As shown in the document of the function: Nreplicates: Number of replicates in your data. Expect each group have the same number of replicates. But in my case, there are multiple conditions (> 2) and different replicates among these conditions. How should I set the argument Nreplicates in the Circ.filter function?

thanks,

Shan

Hi dieterich lab,

I was wondering if the p-value given by circTest output in R is adjusted or unadjusted? If unadjusted, is there a way to get the adjusted p?

Thank you,

Dave

When I run Circ.filter with the output from DCC in R I get this error. When I run it from circtools it doesn't appear. Any help would be much appreciated.

ivan