Question: maSigPro warnings in glm.fit
0
gravatar for Assa Yeroslaviz
3.4 years ago by
Assa Yeroslaviz1.2k
Munich
Assa Yeroslaviz1.2k wrote:

Hi,

I am working on a RNA-Seq data set from drosophila melanogaster time course analysis. I am trying to computer a regression fit for each of the genes.

when computing the p-values I am getting multiple warnings like this:

There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge

I was wondering what causes this warning and is it essential to change some parameters for better results.

thanks

Assa

 

my edesign is this:

sampleName    Time    Replicates    Group
IFM_Myoblast_1    0    1    1
IFM_Myoblast_2    0    1    1
IFM_Myoblast_3    0    1    1
IFM16h_1    16    2    1
IFM16h_2    16    2    1
IFM16h_3    16    2    1
IFM24h_1    24    3    1
IFM24h_2    24    3    1
IFM24h_3    24    3    1
IFM30h_1    30    4    1
IFM30h_2    30    4    1
IFM48h_1    48    5    1
IFM48h_2    48    5    1
IFM48h_3    48    5    1
IFM72h_1    72    6    1
IFM72h_2    72    6    1
IFM90h_1    90    7    1
IFM90h_2    90    7    1
IFM100h_1    100    8    1
IFM100h_2    100    8    1
warning masigpro glm.fit rnaseq • 1.2k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Assa Yeroslaviz1.2k

Hi Assa,

Did you get any answer to your question? I have the same kind of design, also in D. melanogaster, and get the same error message. Also, when I use next the T.fit() function, I get the following error : [1] "fitting gene 100 out of 1061" [1] "fitting gene 200 out of 1061" [1] "fitting gene 300 out of 1061" [1] "fitting gene 400 out of 1061" [1] "fitting gene 500 out of 1061" [1] "fitting gene 600 out of 1061" [1] "fitting gene 700 out of 1061" [1] "fitting gene 800 out of 1061" Error: object 'lastname' not found

I don't know if it is due to the warning message or if there is another problem.

Thank your for your help.

Stephanie

ADD REPLYlink written 2.8 years ago by Stephanie0

sorry, but no. As it was only a warning, I sort of ignored it.

ADD REPLYlink written 2.8 years ago by Assa Yeroslaviz1.2k
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