Indexing Tables erros during readcufflinks

Question

[nasim.zeeshan25]

Hi,

Here is a problem ("attributes are not identical across measure variables; they will be dropped")that I face while running the readcufflinks command.

> cuff_data<-readCufflinks('/users/Zeeshan/Desktop/cuff')
Creating database /users/Zeeshan/Desktop/cuff/cuffData.db
Reading Run Info File /users/Zeeshan/Desktop/cuff/run.info
Writing runInfo Table
Reading Read Group Info  /users/Zeeshan/Desktop/cuff/read_groups.info
Writing replicates Table
Reading Var Model Info  /users/Zeeshan/Desktop/cuff/var_model.info
Writing varModel Table
Reading /users/Zeeshan/Desktop/cuff/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /users/Zeeshan/Desktop/cuff/gene_exp.diff
Writing geneExpDiffData table
Reading /users/Zeeshan/Desktop/cuff/promoters.diff
Writing promoterDiffData table
Reading /users/Zeeshan/Desktop/cuff/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in /users/Zeeshan/Desktop/cuff/genes.read_group_tracking
Writing geneReplicateData table
Reading /users/Zeeshan/Desktop/cuff/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /users/Zeeshan/Desktop/cuff/isoform_exp.diff
Writing isoformExpDiffData table
Reading /users/Zeeshan/Desktop/cuff/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in /users/Zeeshan/Desktop/cuff/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /users/Zeeshan/Desktop/cuff/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /users/Zeeshan/Desktop/cuff/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /users/Zeeshan/Desktop/cuff/splicing.diff
Writing splicingDiffData table
Reading /users/Zeeshan/Desktop/cuff/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in /users/Zeeshan/Desktop/cuff/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /users/Zeeshan/Desktop/cuff/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /users/Zeeshan/Desktop/cuff/cds_exp.diff
Writing CDSExpDiffData table
Reading /users/Zeeshan/Desktop/cuff/cds.diff
Writing CDSDiffData table
Reading /users/Zeeshan/Desktop/cuff/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in /users/Zeeshan/Desktop/cuff/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

Can anyone help me out here?

Answer 1

[jc.szamosi]

I'm getting the same warning. I wish the message was more informative (which attributes, which variables). I have no idea if this is something I should be worrying about or not. Presumably I'm losing some information, but how much?

Answer 2

[jc.szamosi]

Okay, I think I've figured this out. It looks like this is a warning that reshape2's `melt()` function produces when you're trying to melt different factor columns into a single value column. I suspect (haven't dug through the source) `readCufflinks()` is using `melt()` internally when it creates the SQLite DB. All this means is that the factors are coerced to strings before the melt happens. If I'm right, you can safely ignore these warnings.

If the writers/maintainers of cummerBund wanted to they could probably clean up this error by coercing factors to strings explicitly, but I can see that it would be low-priority.

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