When can we expect the last damn microarray paper?

January 18, 2012
By

(This article was first published on Jermdemo Raised to the Law, and kindly contributed to R-bloggers)

With bonus R code

It came as a shock to learn from PubMed that almost 900 papers were published with the word "microarray" in their titles last year alone, just 12 shy of the 2010 count. More alarming, many of these papers were not of the innocuous "Microarray study of gene expression in dog scrotal tissue" variety, but dry rehashings along the lines of "Statistical approaches to normalizing microarrays to the reference brightness of Ursa Minor".

It's an ugly truth we must face: people aren't just using microarrays, they're still writing about them.

See for yourself:

getCount<-function(term){function(year){
nihUrl<-concat("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",term,"+",year,"[pdat]")
#cleanurl<-gsub('\\]','%5D',gsub('\\[','%5B',x=url))
#http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=microarray%5btitle%5d+2003%5bpdat%5d
xml<-xmlTreeParse(URLencode(nihUrl),isURL=TRUE)
#Data Mashups in R, pg17
as.numeric(xmlValue(xml$doc$children$eSearchResult$children$Count$children$text))
}}

years<-1995:2011
df<-data.frame(type="obs",year=years,
mic=sapply(years,function(x){do.call(getCount('microarray[title]'),list(x))}),
ngs=sapply(years,function(x){do.call(getCount('"next generation sequencing"[title] OR "high-throughput sequencing"[title]'),list(x))})
)
#papers with "microarray" in title
> df[,c("year","mic")]
year mic
1 1995 2
2 1996 4
3 1997 0
4 1998 7
5 1999 28
6 2000 108
7 2001 273
8 2002 553
9 2003 770
10 2004 1032
11 2005 1135
12 2006 1216
13 2007 1107
14 2008 1055
15 2009 981
16 2010 909
17 2011 897
Reading another treatise on microarray normalization in 2012 would be just tragic. Who still reads these? Who still writes these papers? Can we stop them? If not, when can we expect NGS to wipe them off the map?

#97 is a fair start
df<-subset(df,year>=1997)
mdf<-melt(df,id.vars=c("type","year"),variable_name="citation")

c<-ggplot(mdf,aes(x=year))
p<-c+geom_point(aes(y=value,color=citation)) +
ylab("papers") +
stat_smooth(aes(y=value,color=citation),data=subset(mdf,citation=="mic"),method="loess") +
scale_x_continuous(breaks=seq(from=1997,to=2011,by=2))
print(p)
Here I plot both microarray and next-generation sequencing papers (in title). We see kurtosis is working in our favor, and LOESS seems to agree!
But when will the pain end? Let us extrapolate, wildly.

#Return 0 for negative elements
# noNeg(c(3,2,1,0,-1,-2,2))
# [1] 3 2 1 0 0 0 2
noNeg<-function(v){sapply(v,function(x){max(x,0)})}

#Return up to the first negative/zero element inclusive
# toZeroNoNeg(c(3,2,1,0,-1,-2,2))
# [1] 3 2 1 0
toZeroNoNeg<-function(v){noNeg(v)[1:firstZero(noNeg(v))]}

#return index of first zero
firstZero<-function(v){which(noNeg(v)==0)[1]}

#let's peer into the future
df.lo.mic<-loess(mic ~ year,df,control=loess.control(surface="direct"))

#when will it stop?
mic_predict<-as.integer(predict(df.lo.mic,data.frame(year=2012:2020),se=FALSE))
zero_year<-2011+firstZero(mic_predict)
cat(concat("LOESS projects ",sum(toZeroNoNeg(mic_predict))," more microarray papers."))
cat(concat("The last damn microarray paper is projected to be in ",(zero_year-1),"."))

#predict ngs growth
df.lo.ngs<-loess(ngs ~ year,df,control=loess.control(surface="direct"))
ngs_predict<-as.integer(predict(df.lo.ngs,data.frame(year=2012:zero_year),se=FALSE))

pred_df<-data.frame(type="pred",year=c(2012:zero_year),mic=toZeroNoNeg(mic_predict),ngs=ngs_predict)
df2<-rbind(df,pred_df)

mdf2<-melt(df2,id.vars=c("type","year"),variable_name="citation")

c2<-ggplot(mdf2,aes(x=year))
p2<-c2+geom_point(aes(y=value,color=citation,shape=type),size=3) +
ylab("papers") +
scale_y_continuous(breaks=seq(from=0,to=1600,by=200))+
scale_x_continuous(breaks=seq(from=1997,to=zero_year,by=2))
print(p2)

LOESS projects 2038 more microarray papers.
The last damn microarray paper is projected to be published in 2016.

Yeah, right...

Full R code here: https://gist.github.com/1637248

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