input-rna returns zero fold-change from non-rsem input

[umasstr]

Given a 2-column input .tsv (from kallisto abundance.tsv or abundance.h5 processed by sleuth), import-rna generates a .cnr with zero log fold-change for every gene. If normalization is excluded from the code then input-rna returns non-zero values.

I would appreciate any insight as to why values may be thrown out at the quantile step of normalization.

[etal]

How many samples did you use? If just one, then it normalizes against itself and the result is all zeros. (I'll see about improving the error reporting there.)

[umasstr]

This is using four samples with this command: cnvkit.py import-rna -f counts -g ~/cnvkit/data/ensembl-gene-info.mm10.tsv -o ~/output /data/sample1/abundance.tsv /data/sample2/abundance.tsv /data/sample3/abundance.tsv /data/sample4/abundance.tsv.

Lines in the gene info file look something like this:
ENSMUSG00000102693 34.2056074766 1 3073253 3074322 4933401J01Rik 0 1070 tsl5
ENSMUSG00000064842 36.3636363636 1 3102016 3102125 Gm26206 1 110 tsl5
ENSMUSG00000051951 50.1375894331 1 3205901 3671498 Xkr4 2 465598 tsl5
ENSMUSG00000102851 39.7916666667 1 3252757 3253236 Gm18956 3 480 tsl5

and the sample abundance files look like this:
ENSMUSG00000102693 0.006857
ENSMUSG00000064842 0.000000
ENSMUSG00000051951 0.078329
ENSMUSG00000102851 0.019840

they are TPMs, I have also tried multiplying them by the read depth to approximate number of counts, and have also tried the --no-txlen and --no-gc flags but all combinations produce .cnr files with weights of 1 for all genes and log fold-change values of 0 for all genes.

[umasstr]

hg38-based tpms generated by kallisto return a similar normalization problem. However, if I submit .rsem from the same dataset, it works.

[etal]

Thanks for the details, this sounds like a bug in reading the plain 2-column format. I'll look into it.

[etal]

It looks like the 2-column input format is now working with import-rna -f counts in the development version. I'll roll another release.