Error from readCufflinks
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HamidahR • 0
@hamidahr-7049
Last seen 7.8 years ago
United States

Hi All,

I am using the Tuxedo suite for my RNA-seq analysis, and I can finally able to visualize my data using cummeRbund. I got this warning message: "attributes are not identical across measure variables; they will be dropped" after running the code "readCufflinks" in R. I can still perform other downstream codes and generate figures, but I'd like to know if this warning message is of high concern. I attached the full code for you guys to take a look. Any feedback is highly appreciated, thank you very much!

Code:

> Rep1<-readCufflinks("Rep1_withGTF")
Creating database Rep1_withGTF/cuffData.db
Reading Run Info File Rep1_withGTF/run.info
Writing runInfo Table
Reading Read Group Info  Rep1_withGTF/read_groups.info
Writing replicates Table
Reading Var Model Info  Rep1_withGTF/var_model.info
Writing varModel Table
Reading Rep1_withGTF/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading Rep1_withGTF/gene_exp.diff
Writing geneExpDiffData table
Reading Rep1_withGTF/promoters.diff
Writing promoterDiffData table
Reading Rep1_withGTF/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in Rep1_withGTF/genes.read_group_tracking
Writing geneReplicateData table
Reading Rep1_withGTF/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading Rep1_withGTF/isoform_exp.diff
Writing isoformExpDiffData table
Reading Rep1_withGTF/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in Rep1_withGTF/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading Rep1_withGTF/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading Rep1_withGTF/tss_group_exp.diff
Writing TSSExpDiffData table
Reading Rep1_withGTF/splicing.diff
Writing splicingDiffData table
Reading Rep1_withGTF/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in Rep1_withGTF/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading Rep1_withGTF/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading Rep1_withGTF/cds_exp.diff
Writing CDSExpDiffData table
Reading Rep1_withGTF/cds.diff
Writing CDSDiffData table
Reading Rep1_withGTF/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in Rep1_withGTF/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped
2: attributes are not identical across measure variables; they will be dropped
3: attributes are not identical across measure variables; they will be dropped
4: attributes are not identical across measure variables; they will be dropped
5: attributes are not identical across measure variables; they will be dropped
6: attributes are not identical across measure variables; they will be dropped
7: attributes are not identical across measure variables; they will be dropped
8: attributes are not identical across measure variables; they will be dropped

 

cummerbund • 2.2k views
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Entering edit mode
@zeeshan_ibge-8777
Last seen 7.1 years ago
Korea, Republic Of

Were you able to solve this problem???? I am having the same problem

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jc.szamosi ▴ 10
@jcszamosi-9539
Last seen 4 months ago
Canada

I've done a bunch of googling, and this is what I now believe:

This error is coming from the reshape2 package, which readCufflinks uses. The explanation is below, but basically, it's fine. You're just coercing factors into strings. If the authors of cummeRbund wanted to, they could tidy this up, but this is a warning you can safely ignore.

http://stackoverflow.com/questions/25688897/reshape2-melt-warning-message

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Entering edit mode
@dusanrandjelovic-10633
Last seen 6.4 years ago

I had similar problem, but with error on the step Indexing Tables (execution halted). After a while I checked:

cuff <- readCufflinks("<dir>")
obj.fpkm <- repFpkmMatrix(genes(cuff), fullnames=T)
colSums(obj.fpkm)

..and there were all zeros :). Maybe this could shed some light on someone's problem.

Cheers!

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