**30**wrote:

Hi,

I am a Student currently trying to learn and to understand how to analyse microarray data with R and Bioconductor.

I am following this course : https://www.bits.vib.be/training/111-bits/training/previous-trainings/177-microarray-bioconductor

I am currently in the second part, but I already noticed some problems when doing the following :

tab = topTable(data.fit.eb,coef=2,number=2000,adjust.method="BH") topups = tab[tab[, "logFC"] > 1, ] colnames(topups) IDsup = topups$ID

The last line does not work since ID column has been remplaced by the ID in the rownames, so I worked this out alone.

But now I have trouble with this part :

data.fit.con = contrasts.fit(data.fit,contrast.matrix) data.fit.con.eb = eBayes(data.fit.con) results = decideTests(data.fit.con.eb,method='global',adjust.method="BH",p.value=0.05,lfc=1) res.IDsExvsCup = data.fit.con.eb$genes[results[,1]==1,1] res.IDsExvsCdown = data.fit.con.eb$genes[results[,1]==-1,1]

Because I get this :

> res.IDsExvsCup NULL > res.IDsExvsCdown NULL

mostly because "genes" doesn't exist in the MArrayLM data.fit.con.eb :

> names(data.fit.con.eb) [1] "coefficients" "rank" "assign" "qr" [5] "df.residual" "sigma" "cov.coefficients" "stdev.unscaled" [9] "Amean" "method" "design" "contrasts" [13] "df.prior" "s2.prior" "var.prior" "proportion" [17] "s2.post" "t" "df.total" "p.value" [21] "lods" "F" "F.p.value"

I don't see what they want to refer to here ? Is it again to be replaced by rownames() ? but how ?

Please help :)

Thanks

**18k**• written 22 months ago by giroudpaul •

**30**