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closeMissing data
Posted by MIRG on 08 Jul 2012 at 19:53 GMT
Three months after the publication of this article, NCBI's GSE36489 deposit is unavailable. Thus it is impossible to figure out the fold changes for the differentially expressed genes here identified given that these data were not included in table S1. That authors' "ultimate objective" was not a quantitative analysis does not mean that fold changes data are not to be shown and also that microarrays validation by a complementary technique was not to be performed. It is also uncommon to make public only 36 out of the 55 genes identified in the microarrays study. After all this is showing a partial view.
RE: Missing data
wibble replied to MIRG on 09 Jul 2012 at 09:39 GMT
Hi Mirg
I'll get onto GEO and make sure that data is made available.
RE: Missing data
JTon-468 replied to MIRG on 09 Jul 2012 at 10:07 GMT
We apologize for the fact that NCBI GEO has not yet released the P. putida KT2440 transcriptome dataset, which presents fold-change values of all differentially expressed probesets. The dataset is scheduled to for release on Nov 24 2012 (see: http://www.ncbi.nlm.nih.g...). As was already mentioned in the response by Wibble, we will try to expedite this release.
We nevertheless object to this reviewer's opinion that our study is presenting a "partial view", merely because of a delay in the release of the transcriptome dataset. As was clearly emphasized in the discussion section of our paper, the transcriptome data served to provide a global impression of the bacterial response to DIMBOA. Predictions from this transcirptome anlaysis were confirmed with evidence from targeted experiments. If the reviewer cannot wait until the transcriptome dataset is officially released by NCBI, he/she is more than welcome to contact the corresponding authors for the data file.