Reader Comments
Post a new comment on this article
Post Your Discussion Comment
Please follow our guidelines for comments and review our competing interests policy. Comments that do not conform to our guidelines will be promptly removed and the user account disabled. The following must be avoided:
- Remarks that could be interpreted as allegations of misconduct
- Unsupported assertions or statements
- Inflammatory or insulting language
Thank You!
Thank you for taking the time to flag this posting; we review flagged postings on a regular basis.
closemajority genes being expressed highly in normal lung is not evident from data
Posted by mnandita on 05 Nov 2009 at 05:30 GMT
we found that the majority of genes were on average expressed at higher levels in the normal samples.
http://plosmedicine.org/article/info:doi/10.1371/journal.pmed.0030486#article1.body1.sec3.sec4.p2
As per data in table S3, it seems like only 50%, and not a majority of the 94 significantly differentially expressed genes between tumor and normal are expressed at higher levels in the normal samples. (fold difference of geom. means < 1)
RE: majority genes being expressed highly in normal lung is not evident from data
dsshames replied to mnandita on 16 Nov 2009 at 22:13 GMT
The sentence referred to in this comment addresses figure 5, whereas the author of this comment has incorrectly assumed Figure 5 is derived from the supplementary table S3. The text clearly states:
After extracting the relevant probes and filtering the data, we found that the majority of genes were on average expressed at higher levels in the normal samples. While marked gene expression differences between NSCLC and normal lung are to be expected, the 5-aza induction gene set clearly distinguished these phenotypes in our data (Figure 5).
i.e. the “majority” of genes we refer to is in figure 5, as demarked by the dendogram on the vertical axis. Thus the data in figure 5 do support the use of the word majority. However, the next sentence, which refers to Table S3 and where we make no mention of a “majority” of genes, simply states that 94/117 were differentially regulated by SAM:
Of 117 unique genes in this group, 94 were differentially expressed between tumor and benign tissue based on the SAM algorithm (90th percentile confidence, false discovery rate among the 94 significant genes was 0.11 and the delta value used to identify significant genes was 0.54) (Table S3).