Warnings using Galaxy and local CummeRbund

[masefieldcourt]

Hello everyone,

Using Galaxy and a reference genome, I have run the TopHat>Cufflinks>Cuffdiff pipeline on 12 single-end Illumina RNA-seq samples (one control condition and three treatments, 3 biological replicates each).

I have content in the outputs from galaxy so that I can see clearly log fold changes, p-values, accession/transcript name, and so on.

I downloaded all of the output files and changed the names according to the table below and attempted to run it in cummeRbund (in Rstudio) using the command:

> cuff_data<-readCufflinks('C:/Users/me/Documents/RNA-seq/CuffDiff Output')

and I receive the following warnings:

1: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier().
2: Column name mismatch, columns will be matched by position. This warning may be converted to an error soon.
3: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
4: attributes are not identical across measure variables; they will be dropped
5: Named parameters not used in query: log2.fold_change.
6: Named parameters not used in query: gene_id, sample_1, sample_2, status, value_1, value_2, sqrt.JS., test_stat, p_value, q_value, significant
7: Named parameters not used in query: tracking_id, gene_id, CDS_id, gene_short_name, tss_id, class_code, nearest_ref_id, locus, length, coverage
8: attributes are not identical across measure variables; they will be dropped
9: Named parameters not used in query: tracking_id, sample_name, fpkm, conf_hi, conf_lo, status
10: Named parameters not used in query: test_id, sample_1, sample_2, status, value_1, value_2, log2.fold_change., test_stat, p_value, q_value, significant
11: Named parameters not used in query: tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, locus, length, coverage
12: attributes are not identical across measure variables; they will be dropped
13: Named parameters not used in query: tracking_id, sample_name, fpkm, conf_hi, conf_lo, status
14: Named parameters not used in query: test_id, sample_1, sample_2, status, value_1, value_2, log2.fold_change., test_stat, p_value, q_value, significant
15: Named parameters not used in query: test_id, gene_id, sample_1, sample_2, status, value_1, value_2, sqrt.JS., test_stat, p_value, q_value, significant

Does anybody know if it's possible to use the Galaxy data output to use cummeRbund locally? This would be preferred to using cummeRbund in Galaxy. I am using Windows 10, and the latest versions of both Rstudio and cummeRbund. SQLite confuses me, but I think I have the latest version since I have installed the package RSQLite using the Rstudio software manager.

Any help would go a long ways and be greatly appreciated. Thank you for your time.
-A

[Aurita]

Same error

I jsut got that same error, were you able to figure out how to solve it? I am using Windows 7, and just re-installed the latest R and cummerbund