erro Now summarizing method=CbMPDiCbraya i=1 j=1. Sat Mar 9 23:34:20 2024 Error in oldname[j, 1:2] : subscript out of bounds about icamp1 HOT 11 OPEN

@xuyangr You can download the latest version of iCAMP from https://github.com/DaliangNing/iCAMP1/tree/master/RPackage/AllVersions.

Sorry, I do not fully understand your question. I guess you have 'relative abundance' data where the sum of each sample is 100%. If so, you may set dirichlet=TRUE in icamp.big, see step 9.5 in example R code https://github.com/DaliangNing/iCAMP1/blob/master/Examples/SimpleOTU/icamp.test.r.
If you mean you are not able to install iCAMP recent versions with the ability to handle relative abundance data, you can try to transform the community data to "count" data table, e.g., dividing the whole matrix by the minimum positive number in the matrix, then round to integers.

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This error was usually because there was only one treatment, but 'between.group=TRUE'. Please check your 'treat' table; if there is only one group (treatment), please set between.group=FALSE; if there is multiple groups (treatments), please send me ([email protected]) icres, treat, clas (save them as rda files) to debug.

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@DaliangNing Hello professor,I had the same error and I saw the solution you gave was: set between.group=FALSE. I followed the tutorial on IEG3 and I don't know how to set "set between.group=FALSE".

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@makerer5 In the function 'iCAMP' on our web-based pipeline (http://ieg3.rccc.ou.edu:8080/), the option 'Summarize for between-group turnovers?' is about 'between.group', and the default setting is 'No' which means 'between.group=FALSE'. If you used default setting, your error is probably not due to 'between.group' setting. You may let me know your username on the pipeline to debug, or explore R package version.

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@DaliangNing Hello professor,My username in IEG3 is '' [email protected]'', and my working environment is ''fungi''. I am also trying to use R code to explore the results when treatment is a group

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@makerer5 the problem is solved. You may check the latest result files in your galaxy pipeline history 'fungi'.

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The error on Galaxy pipeline can happen when all samples are belong to the same group. I have revised the backend script to consider this kind of special cases.

Similarly, when using the function icamp.boot in R package, if there is only one group, you need to set compare as FALSE; otherwise, the function will only return similar error.

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@Panda-smile sorry for my late response. Your error is caused by 'treat'.
iCAMP is based on beta diversity (pairwise dissimilarity between samples), thus each group must have at least 2 samples to provide between-sample beta diversity. Actually, a group had better include 6 or more samples to get relatively reliable null model estimations. But your 'treat' table (below) has multiple groups that only have a single sample.

treat
Management Location
FQ1 FQ1 Qu
FQ2 FQ2 Qu
CP CP Qu
SC SC Qu
DJ DJ Fermentation

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dear professor, I am having problems running icamp because my version of icamp is too low, but input is a abundance file so it is less than 1. In the case of not updating the version, I would like to know whether it is possible to directly expand the abundance data by 100,000 times as the input file, so that the results of the calculation will be affected? Looking forward to your reply
.

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Dear Professor:
I encountered the following issues when conducting diversity analysis of iCAMP on Galaxy. I am not sure where the problem lies. Could you show and help me figure it out? My account is [email protected]. I am looking forward to your reply. Thank you so much.

Fatal error: Exit code 1 ()
Now computing path. begin at Sat May 11 22:04:08 2024. Please wait...
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: subscript out of bounds
Calls: ... clusterApply -> staticClusterAp

Your Sincerely
Kerry

@xuyangr You can download the latest version of iCAMP from https://github.com/DaliangNing/iCAMP1/tree/master/RPackage/AllVersions.

Sorry, I do not fully understand your question. I guess you have 'relative abundance' data where the sum of each sample is 100%. If so, you may set dirichlet=TRUE in icamp.big, see step 9.5 in example R code https://github.com/DaliangNing/iCAMP1/blob/master/Examples/SimpleOTU/icamp.test.r. If you mean you are not able to install iCAMP recent versions with the ability to handle relative abundance data, you can try to transform the community data to "count" data table, e.g., dividing the whole matrix by the minimum positive number in the matrix, then round to integers.

from icamp1.