Error in .normargSEW0(start, "start") error

[Shawnmhy]

Error in .normargSEW0(start, "start") error

[chrisamiller]

Try removing the header line from your VAF file

[Shawnmhy]

Try removing the header line from your VAF file

But the VAF file in your example also has header line.

[chrisamiller]

Possibly the CN file, then? I'm away today, and can't verify, but I recall that headers on one of the input files can have that effect. If that doesn't solve it, let me knoe

[Shawnmhy]

Neither my CN file nor VAF file has headers but the error is still there...

[Shawnmhy]

ok now the error is gone, but when I delete headers another issue came:

Error in cleanAndAddCN(vafs[[i]], copyNumberCalls[[i]], i, cnCallsAreLog2, :

[Shawnmhy]

I am just running one sample, but seems like I also need to proved other two samples:

[1] "ERROR: column st in sample 2 is not numeric"

[chrisamiller]

Were you able to figure this out? If so, I'm going to resolve this issue - thanks

[Shawnmhy]

Yes I figured this out! Thanks!

[jfass]

I am just running one sample, but seems like I also need to proved other two samples:

[1] "ERROR: column st in sample 2 is not numeric"

@Shawnmhy how did you address the "column st in sample 2 is not numeric" error? I'm also using a single sample at a time (no multi-sequenced tumors), and I'm getting this error.

EDIT: nevermind; the positions in the vaf data frame were still characters!

[chrisamiller]

Try removing any non-numeric characters (including headers) from your input list.