[R-sig-ME] lme4 analysis_2ANOVA repeated measure
Tanay Ghosh
tg369 @end|ng |rom c@m@@c@uk
Thu Jun 13 23:16:27 CEST 2019
Dear Emmanuel,
Many thanks for this reply.
I now added a column "subject id" (attached).
Atg3 is the name of a gene whose expression level was measured.
I know that we can not detect any difference here, also aware of the
outlier. However, using this data set as an example, I want to learn
using lme4 for RM ANOVA specially when some values are NA.
Please do not hesitate to ask if anything is unclear and I am looking
forward to hearing from you.
Kind regards,
Tanay
On 2019-06-13 13:45, Emmanuel Curis wrote:
> Hi Tanay,
>
> In your data file, there seems to be nothing like « subject id », but
> only time, sex and Atg3 (=Abt3 ?) measure so it's not possible to do
> any random-effect modeling.
>
> Besides, you should give more explaination about what is the Atg3
> column, because the syntax will change if there are CTs or equivalent
> measures [does not look like, except the atypical 31.355 value],
> absolute quantities or relative quantities compared to a (set of)
> reference genes.
>
> Last, comparing all times to see a time effect is not a very powerful
> method, because you quickly increase the number of comparisons, and at
> the extreme, the more time you have, the more precise is your time
> curve, the more difficult it is to detect anything...
>
> Note however that looking « by eye » your data, you can't expect much
> since you have a small dataser, huge outliers (31.355, 5.081, 4.804)
> and a quite high intra-groupe variability (values ranging from 0.087
> to 2.237 for the 3 males at t=7, for instance).
>
> est regards,
>
> On Mon, Jun 10, 2019 at 03:31:53PM +0100, Tanay Ghosh wrote:
> « Dear All,
> «
> « I wonder if I can ask your advise to analyse this data (attached).
> Please
> « note that some of the values are "NA" i.e. I do not have any
> measurement
> « taken.
> «
> « Here I have four different time (days) points. I measured expression
> of Abt3
> « gene at these time points in male and female.
> «
> « I want to see if gender wise expression of Atg3 differ at any time
> point?
> «
> « I further want to do a posttest to get p value for Male at time 7 vs
> female
> « at time 7, Male at time 15 vs Female at time 15, and like wise all
> other
> « time points.
> «
> «
> « Please could you advise me how to do this analysis using lmer
> function? I
> « would very much appreciate if you please write the commands in R for
> this
> « specific case.
> «
> « Thank you in advance for your time.
> «
> «
> « Kind regards,
> «
> « Tanay
> «
> «
> « --
> « Dr. Tanay Ghosh, PhD
> « Research Associate
> « Department of Clinical Neurosciences,
> « Wellcome Trust-Medical Research Council Cambridge Stem Cell
> Institute,
> « Clifford Allbutt Building,
> « Cambridge Biomedical Campus,
> « University of Cambridge,
> « Cambridge CB2 0AH
>
> «
> time Gender Atg37 Male 0.2127 Male 2.2377 Male 0.0877 Female 0.0927 Female 2.8057 Female 0.10315 Male 0.07115 Male 2.73315 Male 2.41415 Female 0.1515 Female 2.43815 Female 1.43424 Male 0.07924 Male 2.21224 Male 31.35524 Female 0.21124 Female 0.81224 Female 5.081231 Male 0.073231 Male 0.505231 Male 0.737231 Female 0.178231 Female 0.319231 Female 4.804420 Male 0.29420 Male 0.424420 Male NA420 Female 0.337420 Female 0.966420 Female NA
>
> « _______________________________________________
> « R-sig-mixed-models using r-project.org mailing list
> « https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
--
Dr. Tanay Ghosh, PhD
Research Associate
Department of Clinical Neurosciences,
Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute,
Clifford Allbutt Building,
Cambridge Biomedical Campus,
University of Cambridge,
Cambridge CB2 0AH
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