Error in chromosome 1

[ramonv...@gmail.com]

Hello again Yuchao,

Being getting this error only in chromosome 1:

After taking union, excluded 10358 out of 229611 exons in QC.

Error in smooth.spline(gc_qc, z) : 

  'tol' must be strictly positive and finite

Calls: normalize_null -> normalize -> apply -> FUN -> smooth.spline

In addition: Warning messages:

1: In matrix(nrow = nrow(Y_qc), ncol = ncol(Y_qc), data = N, byrow = TRUE) :

  data length exceeds size of matrix

2: In matrix(nrow = nrow(Y_qc), ncol = ncol(Y_qc), data = N, byrow = TRUE) :

  data length exceeds size of matrix

Execution halted

I didn't loose all my data after QC, so I was wandering what might be happening. Do you have any suggestions?

Thanks for your patience,

Ramon

[Yuchao Jiang]

It’s hard to tell just based on this. Check if there any missing values or negative values in your gc content?

Sent from my iPhone

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[ramonv...@gmail.com]

Just checked the qcmat file, there is no missing values or negative results in gc line, the minimum gc is 19.67 and maximum is 83.91 for chr1. Maybe the file formatting could lead to an error while reading the lines? 

Em segunda-feira, 15 de julho de 2019 16:41:12 UTC-3, Yuchao Jiang escreveu:

It’s hard to tell just based on this. Check if there any missing values or negative values in your gc content?

Sent from my iPhone

On Jul 15, 2019, at 2:17 PM, ramonv...@gmail.com wrote:

Hello again Yuchao,

Being getting this error only in chromosome 1:

After taking union, excluded 10358 out of 229611 exons in QC.

Error in smooth.spline(gc_qc, z) : 

  'tol' must be strictly positive and finite

Calls: normalize_null -> normalize -> apply -> FUN -> smooth.spline

In addition: Warning messages:

1: In matrix(nrow = nrow(Y_qc), ncol = ncol(Y_qc), data = N, byrow = TRUE) :

  data length exceeds size of matrix

2: In matrix(nrow = nrow(Y_qc), ncol = ncol(Y_qc), data = N, byrow = TRUE) :

  data length exceeds size of matrix

Execution halted

I didn't loose all my data after QC, so I was wandering what might be happening. Do you have any suggestions?

Thanks for your patience,

Ramon

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