Question: kissDE diffExpressedVariants Error in nls
0
gravatar for ovidiu
18 days ago by
ovidiu0
Germany
ovidiu0 wrote:

Dear Community,

I try to use kissDE diffExpressedVariants on a count table from paired end RNA Seq Data. The input file is kissplice type0a format. I have 4 samples with three replicates each. When I try to run diffExpressedVariants I get the following error. Any suggestions are welcome! Thank you!

Error in nls(modelNB, data = event.mean.variance.df, start = list(theta = 100)): step factor 0.000488281 reduced below 'minFactor' of 0.000976562\n An error occured, unable to fit models on data.


head(snp$countsEvents)
       events.names events.length counts1 counts2 counts3 counts4 counts5 counts6 counts7 counts8 counts9 counts10 counts11
1 bcc_99967|Cycle_0            83      50      55      35       0       0       0      77      66      75        0        0
2 bcc_99967|Cycle_0            83       0       0       0      82      88      88       0       0       0       45       33
3 bcc_99898|Cycle_0            83       0       0       0      52      62      59       0       0       0       25       37
4 bcc_99898|Cycle_0            83      52      37      67       0       0       0      49      76      49        0        0
5 bcc_99803|Cycle_0            83       0       0       0     113     121     153       0       0       0       81      122
6 bcc_99803|Cycle_0            83     110      70      81       0       0       0      62      85      82        0        0

  counts12
1        0
2       76
3       39
4        0
5      116
6        0
kissplice snp rna-seq • 115 views
ADD COMMENTlink modified 11 days ago • written 18 days ago by ovidiu0
0
gravatar for ovidiu
17 days ago by
ovidiu0
Germany
ovidiu0 wrote:

UPDATE

I found out is that the error is caused by the starting value (theta=100) when calling the nls function Letting nls doing the cheap guessing of the starting values solves the problem.

I'm not sure how this changes the results at the end.

ADD COMMENTlink modified 17 days ago • written 17 days ago by ovidiu0
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