Closed:Voom: need at least two non-NA values to interpolate

Question

[komal.rathi]

Hi,

I am trying to apply voom to expected counts from RSEM FPKM (I don't have raw counts). My next step is to compute a differential test using limma.

# matrix I am trying to apply voom to has 1 row and 8021 columns:
> dim(tmp)
[1]    1 8021

# first five columns
> tmp[,1:5]
                    SRR1068687 SRR1068788 SRR1068808 SRR1068832 SRR1068855
ENSG00000149294.16     2528.61     756.53         36     158.95    1652.77

# no NAs in the matrix
> whichis.na(tmp))
integer(0)

# this is my design. shows that I have replicates.
> rbind(head(design),tail(design))

                                     studyGTEx studyTARGET
SRR1068687                                   1           0
SRR1068788                                   1           0
SRR1068808                                   1           0
SRR1068832                                   1           0
SRR1068855                                   1           0
SRR1068880                                   1           0
f3b75630.42da.4b66.96c5.94e9a8142261         0           1
f62f350c.f8b5.4715.ace1.387f7e59cb91         0           1
f637ca92.407d.432e.ba08.2bebe05b96f4         0           1
f835cce2.1ed3.4c59.95a2.4bfef161082b         0           1
fb8c3046.eb74.43ff.ae1d.327453221555         0           1
fdee8bef.5ce2.4ca6.b6b9.3423219a1ea4         0           1

# I get an error when I try to apply voom:
> voom(tmp, design = design)
Error in approxfun(l, rule = 2) : 
  need at least two non-NA values to interpolate

I searched for the error and I found that it is usually encountered when you have no replicates. However in my case I have enough replicates - studyGTEx has about 7000 and the remaining are studyTARGET. What could be the problem?

NOTE: I have already tried adding more rows (to make nrow(tmp)>1) and I still get the same error.

Crossposted: https://support.bioconductor.org/p/86934/