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Question: fourCseq - error getZscores
0
gravatar for samuel collombet
2.7 years ago by
France
samuel collombet120 wrote:

Hi,

When I try to call the function getZSCores on my 4C data (mouse) I got the following error:

> data_fcf <- getZScores(data_fc,minCount=10,fitFun=distFitMonotone)
[1] "VP1"
gene-wise dispersion estimates
mean-dispersion relationship
NOTE: fitType='parametric', but the dispersion trend was not well captured by the
  function: y = a/x + b, and a local regression fit was automatically substituted.
  specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
Error in getZScores(data_fc, minCount = 10, fitFun = distFitMonotone) : 
  Failed to estimate the parameters of the Variance stabilizing transformation.

Looking at the code it seems due to the fact that parametric fit did not work so he stopped after that. 
Is it not possible to go further in the analysis with a local fit?

ADD COMMENTlink modified 2.6 years ago by felix.klein150 • written 2.7 years ago by samuel collombet120
0
gravatar for Wolfgang Huber
2.7 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Hi Samuel

thank you for your interest in this package and for reporting the problem. This should be fixable. Can you send a complete (minimal) code example and your sessionInfo? (Plus perhaps also the required input data, privately).

Kind regards

Wolfgang

 

ADD COMMENTlink written 2.7 years ago by Wolfgang Huber13k
0
gravatar for felix.klein
2.7 years ago by
felix.klein150
Germany
felix.klein150 wrote:

Hi Samuel,

currently the analysis does not work with a local fit. Maybe you can adjust the threshold in the function if you have noisy data.

How do the scatter plots of your replicates look? This should help to find a suitable threshold.

Best regards,

Felix

ADD COMMENTlink written 2.7 years ago by felix.klein150

Hi Felix,

I am running into the same error.

I have no replicate for the sample (since it was a trial) and that could be the cause of error. Is it possible to use the method when there are no replicates?

 

I have another issue when running the example (without including  2R). It gives the error

 Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
  every gene contains at least one zero, cannot compute log geometric means.

 

Best Regards,

Shruti

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by sinhashruti0
0
gravatar for felix.klein
2.6 years ago by
felix.klein150
Germany
felix.klein150 wrote:

Hello Shruti,

you need at least two measurements for a viewpoint to estimate the dispersions. Ideally you have replicates from different conditions.

In the second error it seems like most of your counts are 0 or at least one replicate. Check this by looking at the counts table of your objects:

head(counts(fc), 25)

Best regards,

Felix

 

ADD COMMENTlink written 2.6 years ago by felix.klein150

Hi Felix,

Thank you for the reply. I was thinking since now DESeq can be used on data without replicate, probably there would be some feature to do the same for FourCSeq. 

 

For the second error, below is the result from head(counts(fc),25). Please note that the data is from the example data in the package but excluding the 2R. I wanted to check if it works for single chromosome or not. Is it that it needs a specific number of rows before calculating?

> head(counts(fc), 25)

     testdata_WE_68h_1 testdata_WE_68h_2 testdata_MESO_68h_1 testdata_MESO_68h_2 testdata_WE_34h_1 testdata_WE_34h_2
[1,]                 0                13                   4                   0                 0                 0
[2,]                 6                 0                   0                   2                 8                 0

Best Regards

Shruti

 

ADD REPLYlink written 2.6 years ago by sinhashruti0
0
gravatar for felix.klein
2.6 years ago by
felix.klein150
Germany
felix.klein150 wrote:

Hi Shruti,

the testdata in the package is only included to provide an example on how the fragment reference is generated and how it is counted. Therefore you get errors when running the getZScore function.

If you run it on your own data make sure, that there is not a replicate that only contains 0 counts. If there is, remove it from your analysis.

Best reagards,

Felix

ADD COMMENTlink written 2.6 years ago by felix.klein150
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