Question: miR2Pathway and finite observations
0
gravatar for plink_9857
13 months ago by
plink_985740
United States
plink_985740 wrote:

I am using the miR2Pathway package and have encountered an error message and warning messages that I need help troubleshooting. The finite observations warning is interesting to me, since it alludes to there being too few mirna listed. The input file contains 1,046 miRNAs that are being analyzed and are potentially being reduced to a list of less than 3 miRNAs.

Please visit the following github for the main functions, example input and example usage code:

miR2Pathway: https://github.com/GenomicsPrograms/miR2Pathway

Error and Warning Messages:

[1] 1044

[1] 1045

[1] 1046

[1] "miRtarnetwork step is done!!!"

Error in { : task 7 failed - "not enough finite observations"

In addition: There were 48 warnings (use warnings() to see them)

> warnings()

Warning messages:

1: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

2: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

3: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

4: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

5: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

6: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1245

7: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1260

8: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1268

9: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1269

10: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1273

11: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1274a

12: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1274b

13: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

14: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-1295

15: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

16: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

17: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

18: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

19: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

20: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

21: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

22: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

23: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

24: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-3135

25: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-3150

26: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-3155

27: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

28: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-3647

29: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

30: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

31: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

32: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

33: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

34: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

35: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

36: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

37: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

38: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

39: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

40: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

41: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

42: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

43: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-550b

44: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  no targets found for mirna mir-550b

45: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

46: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

47: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1

48: In getPredictedTargets(miRlist[i], species = "hsa", method = "geom",  ... :

  sources which returned a target list<min_src, min_src reduced to 1



sessionInfo()

> sessionInfo() <br>
R Under development (unstable) (2018-03-10 r74380) <br>
Platform: x86_64-w64-mingw32/x64 (64-bit) <br>
Running under: Windows 10 x64 (build 16299) <br>

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
 [1] stats4    parallel  compiler  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] igraph_1.2.1         graph_1.57.1         graphite_1.25.1      miRNAtap.db_0.99.10  miRNAtap_1.13.0      AnnotationDbi_1.41.4 IRanges_2.13.28     
 [8] S4Vectors_0.17.35    Biobase_2.39.2       BiocGenerics_0.25.3  doParallel_1.0.11    iterators_1.0.9      foreach_1.4.4       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16     pillar_1.2.1     plyr_1.8.4       tools_3.5.0      digest_0.6.15    bit_1.1-12       RSQLite_2.0      memoise_1.1.0   
 [9] tibble_1.4.2     checkmate_1.8.5  pkgconfig_2.0.1  rlang_0.2.0      DBI_0.8          proto_1.0.0      stringr_1.3.0    httr_1.3.1      
[17] rappdirs_0.3.1   bit64_0.9-7      sqldf_0.4-11     R6_2.2.2         gsubfn_0.7       blob_1.1.0       magrittr_1.5     backports_1.1.2
[25] codetools_0.2-15 stringi_1.1.7    chron_2.3-52    



Object list: ls()

 [1] "genelist"      "miR2Pathway"   "miRlist"       "miRlist.full"  "mydata.gene"   "mydata.miR"    "N.gene"        "N.miR"         "N.path"       
[10] "name.genelist" "name.miRlist"
mirna R pathway • 336 views
ADD COMMENTlink modified 13 months ago by genomax65k • written 13 months ago by plink_985740
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1135 users visited in the last hour