jave exception

[wangjiawen2013]

Hi, when I run BMDexpress3 command line interface following the video tutorial (https://www.youtube.com/watch?v=HJPcigf4dTE&list=PLX2Rd5DjtiTeR84Z4wRSUmKYMoAbilZEc&index=21), the belowing error occurred:

Reading expression data Import Expression Data From Directory: data/ Import Expression Data File From Directory: TCP.txt java.lang.NumberFormatException: For input string: "013-051914-MW_(Rat230_2).CEL" at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054) at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122) at java.base/java.lang.Float.parseFloat(Float.java:455) at java.base/java.lang.Float.valueOf(Float.java:419) at com.sciome.bmdexpress2.util.ExperimentFileUtil.readFile(ExperimentFileUtil.java:118) at com.sciome.bmdexpress2.util.ExperimentFileUtil.readFile(ExperimentFileUtil.java:52) at com.sciome.bmdexpress2.commandline.ExpressionImportRunner.runExpressionImport(ExpressionImportRunner.java:23) at com.sciome.bmdexpress2.commandline.AnalyzeRunner.doExpressionConfig(AnalyzeRunner.java:1255) at com.sciome.bmdexpress2.commandline.AnalyzeRunner.analyze(AnalyzeRunner.java:141) at com.sciome.bmdexpress2.commandline.BMDExpressCommandLine.run(BMDExpressCommandLine.java:135) at com.sciome.bmdexpress2.commandline.BMDExpressCommandLine.main(BMDExpressCommandLine.java:75) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84) at com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66) at install4j.com.sciome.bmdexpress2.commandline.BMDExpressCommandLine.main(Unknown Source) java.lang.NullPointerException at com.sciome.bmdexpress2.commandline.ExpressionImportRunner.runExpressionImport(ExpressionImportRunner.java:25) at com.sciome.bmdexpress2.commandline.AnalyzeRunner.doExpressionConfig(AnalyzeRunner.java:1255) at com.sciome.bmdexpress2.commandline.AnalyzeRunner.analyze(AnalyzeRunner.java:141) at com.sciome.bmdexpress2.commandline.BMDExpressCommandLine.run(BMDExpressCommandLine.java:135) at com.sciome.bmdexpress2.commandline.BMDExpressCommandLine.main(BMDExpressCommandLine.java:75) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84) at com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66) at install4j.com.sciome.bmdexpress2.commandline.BMDExpressCommandLine.main(Unknown Source) Error:null usage: bmdexpress3-cmd --version usage: bmdexpress3-cmd analyze --config-file [--veryverbose] --config-file --veryverbose usage: bmdexpress3-cmd export --analysis-group [--analysis-name ] --input-bm2 --output-file-name

[--veryverbose] --analysis-group --analysis-name --input-bm2 --output-file-name

--veryverbose usage: bmdexpress3-cmd delete --analysis-group --analysis-name --input-bm2 [--veryverbose] --analysis-group --analysis-name --input-bm2 --veryverbose usage: bmdexpress3-cmd query --analysis-group --input-bm2 [--veryverbose] --analysis-group --input-bm2 --veryverbose usage: bmdexpress3-cmd combine --input-bm2-files --output-file-name

[--veryverbose] --input-bm2-files --output-file-name

--veryverbose

: expression, anova, williams, curvefit_prefilter, oriogen, bmd, categorica Could you help me find the reason ?

[wangjiawen2013]

I solved it by changing the config file:

[wangjiawen2013]

The expression and config file were from microarray assay, then how about the transcriptome RNAseq ? What should be used as input when using RNAseq data ?

[auerbachs]

You will need to change the platform to either human, mouse, or rat ensemble or refseq (ID to enter is in the ID column in the below image). This is assuming that you are using one of those identifiers in your RNA-seq expression data file.

[wangjiawen2013]

Thanks! Then how to update the above annotations table using command line interface? Does it need a internet connnection to update ? is the annotations table are stored locally so we can use command line interface without a internet connection ?

[wangjiawen2013]

And, where can we find the content of the annotations, such hg38_essemble ID/biospyder ID ? This is necessary because we must map our genes to the annotations, so we must known what the ID looks like in order to preprocess our expression data.

This is ensemle ID:

This is another ensemble ID

So we must determine the ID by browsing the content of the annotations.

[auerbachs]

Currently you have to use the GUI to download/install the annotations.

The Ensembl IDs should look like the following

[wangjiawen2013]

I found the downloaded annotaions in ~/bmdexpress3/data/annotations/, It is what I want to see.