Problem reproducing bulk RNA-seq tutorial results about tradeseqpaper HOT 6 CLOSED

Hi,

What version of tradeSeq are you using?
The code in this repository is based on an older version of tradeSeq, which we've now updated considerably.

It may help to re-run fitGAM by setting sce=FALSE, as in #1 .

from tradeseqpaper.

Hello,

Thank you for the speedy response!
I'm using tradeSeq version 1.2.1 in R version 4.0.0.
I saw the previous post and tried setting sce=FALSE, and this produced the same error as the default sce setting.

from tradeseqpaper.

Thanks. Are you getting a list output from fitGAM? Is the output from is(gamList, "list") equal to TRUE?

from tradeseqpaper.

Yes it is a list:
is(gamList, "list") [1] TRUE

from tradeseqpaper.

Hi @RJoyce-bbk

My apologies for taking so long in getting back to you. I am not having this problem with the latest tradeSeq version (tradeSeq_1.3.15), so you may want to update and check again. My apologies for the inconvenience.

For reference, here is the code I used:

> gamList <- fitGAM(counts, pseudotime=time, cellWeights=weights, 
+                   nknots=6, sce=FALSE)
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=08m 27s
> resPat <- patternTest(gamList, nPoints=8)

from tradeseqpaper.

Closing due to inactivity, feel free to open another issuel

from tradeseqpaper.