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**RE: One sample or t-test**Oct 16, 2018 03:10 AM | Alessio Bellato -

*University of Nottingham*RE: One sample or t-test

Oh I see, I have just tried and it works with lower thresholds.

Thanks very much Andrew!

Regards,

Alessio

Thanks very much Andrew!

Regards,

Alessio

*Originally posted by Andrew Zalesky:*Hi
Alessio,

Try lowering the threshold. Try 0.2 or 0.5, or threshold values in this range.The threshold value for the one-sample t-test is expressed in terms of the mean connectivity across all samples.

If this does not work, check that your connectivity values are indeed positive for the majority of samples.

Andrew

I tried the same analysis (one-sample t-test), on 20 matrices from the same group of typically developing controls. I did it to do a first thresholding on the matrices by testing, within this group, which connections were significantly different from 0.

Here the setup. Test: One-sample; Method: NBS, Sig: 0.05. Threshold: 3. 5000 permutations. The design matrix is as LJ Yin showed, contrast set as [1].

However, when I run the analysis, the Max Size Random, Max Size Actual never change from 0.0, and Lowest p-value never changes from 1.0.

Obviously, there is no significant result.

How is this possible?

What did I do wrong?

Many regards,

Alessio

Try lowering the threshold. Try 0.2 or 0.5, or threshold values in this range.The threshold value for the one-sample t-test is expressed in terms of the mean connectivity across all samples.

If this does not work, check that your connectivity values are indeed positive for the majority of samples.

Andrew

*Originally posted by Alessio Bellato:**Originally posted by LJ Yin:*

Hi Andrew,

I am trying to use NBS to analyze data. I have one group of subjects and I would like to test if the means of some connections are greater than or smaller than zero.

1) I chose one sample as the statistic analysis. And the design matrix is listed as follow:

1

1

1

1

...

I set the contrast of 1. Is this the correct way of performing the analysis?

2) According to the manual, "The one sample test randomly flips the sign of each data point for each permutation, which corresponds to a one-sided, one sample t-test. Note that the one sample test always assesses whether the mean is greater than zero, irrespective of the sign of the contrast vector." I guess the one sample test is only to test the positive effect, right? What if I would like to test both the positive and negative effect?

3) What's the difference between "one-sample" and "t-test"? Shouldn't I obtain the same result by using "one-sample" and "t-test"by applying the same design matrix and contrast like I mentioned above?

Thank you in advance.

Best regards,

Lijun

Hi Andrew, I have a quite similar
question.I am trying to use NBS to analyze data. I have one group of subjects and I would like to test if the means of some connections are greater than or smaller than zero.

1) I chose one sample as the statistic analysis. And the design matrix is listed as follow:

1

1

1

1

...

I set the contrast of 1. Is this the correct way of performing the analysis?

2) According to the manual, "The one sample test randomly flips the sign of each data point for each permutation, which corresponds to a one-sided, one sample t-test. Note that the one sample test always assesses whether the mean is greater than zero, irrespective of the sign of the contrast vector." I guess the one sample test is only to test the positive effect, right? What if I would like to test both the positive and negative effect?

3) What's the difference between "one-sample" and "t-test"? Shouldn't I obtain the same result by using "one-sample" and "t-test"by applying the same design matrix and contrast like I mentioned above?

Thank you in advance.

Best regards,

Lijun

I tried the same analysis (one-sample t-test), on 20 matrices from the same group of typically developing controls. I did it to do a first thresholding on the matrices by testing, within this group, which connections were significantly different from 0.

Here the setup. Test: One-sample; Method: NBS, Sig: 0.05. Threshold: 3. 5000 permutations. The design matrix is as LJ Yin showed, contrast set as [1].

However, when I run the analysis, the Max Size Random, Max Size Actual never change from 0.0, and Lowest p-value never changes from 1.0.

Obviously, there is no significant result.

How is this possible?

What did I do wrong?

Many regards,

Alessio

## Threaded View

Title | Author | Date |
---|---|---|

LJ Yin |
Sep 3, 2018 | |

Alessio Bellato |
Oct 12, 2018 | |

Andrew Zalesky |
Oct 15, 2018 | |

Alessio Bellato |
Oct 16, 2018 | |

Andrew Zalesky |
Sep 3, 2018 | |

LJ Yin |
Sep 5, 2018 | |

Andrew Zalesky |
Sep 6, 2018 | |