Closed DoYup closed 6 years ago
Dear DoYup,
Thank you for contacting again.
First, I am aware that label_compare
does not return p-values and foldchanges as PuInc_seeker
does. I will try to add this feature to the function ASAP (I actually cannot understand why we did not do that in the first place).
The main feature of label_compare
is the first column ('Comparison') which will include "UP" or "DOWN" values when significant results are found. Since I see that when you run
s4 <- label_compare(geoRgeR = s2, XCMSet = xset3, ppm.s = NULL,rt.win.min = 1, control.cond = NULL, fc.vs.Control = 1, p.value.vs.Control = 0.05, Show.bp = T)
you have 'ppm.s' and 'control.cond' set to NULL. This might be the cause that this result comes up:
$ Comparison : Factor w/ 2 levels "","Base peak": 2 1 2 1 1 2 1 2 1 1 ...
Please try to run again this function, like this (or similar):
s4 <- label_compare(geoRgeR = s2, XCMSet =mtbls213, rt.win.min = 1,
control.cond = "05mM_Normo",ppm.s=6.5,
fc.vs.Control = 1, p.value.vs.Control = 0.05, Show.bp = T)
This should return (see number of levels of $ Comparison):
str(s4)
'data.frame': 1105 obs. of 5 variables:
$ Comparison : Factor w/ 4 levels "","Base peak",..: 2 1 2 1 1 2 1 2 1 1 ...
$ X05mM_Normo_MEAN: num 61.89 38.11 81.43 7.36 11.21 ...
$ X25mM_Normo_MEAN: num 67.12 32.88 82.01 7.92 10.07 ...
$ X05mM_Normo_SD : num 7.17 7.17 1.6 0.37 1.92 ...
$ X25mM_Normo_SD : num 0.87 0.87 0.723 0.437 1.142 ...
Last but not least, you indicated that this function does not work for your data. I would like to ask you if at least the % values are calculated.
Yours sincerely,
Jordi
Great. It works.
For my data, % are calculated. I wish to see p value and fold change soon. :) Now I will try to do it with my data. (I may return to you at that moment with question) Thank you again
The package was updated a few weeks ago, the p-value and fold-change should be reportable now. I wonder if you have been able to run it for your data.
Hi Jordi
It sounds great! And it works very well with my real data thanks to your help !!!
Sincerely, Do Yup
On Mon, Aug 28, 2017 at 5:59 PM, Jordi Capellades Tomas < notifications@github.com> wrote:
The package was updated a few weeks ago, the p-value and fold-change should be reportable now. I wonder if you have been able to run it for your data.
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Dear Jordi
Thanks for your help the other day.
I have question on Welch's ttest between different condition. Because my own data is not working I have tried it with example data "mtbl231". But I was not able to have p value and fold change between two condition.
Here is the script I am using. I have tried it with different combination of control.con = (e.g. "05mM_Nor)
Here is the file name that I downloaded for mtbl231 CELL_Glc12_05mM_Normo_04 CELL_Glc12_05mM_Normo_05 CELL_Glc12_05mM_Normo_06 CELL_Glc12_25mM_Normo_16 CELL_Glc12_25mM_Normo_17 CELL_Glc12_25mM_Normo_18 CELL_Glc13_05mM_Normo_01 CELL_Glc13_05mM_Normo_02 CELL_Glc13_05mM_Normo_03 CELL_Glc13_25mM_Normo_13 CELL_Glc13_25mM_Normo_14 CELL_Glc13_25mM_Normo_15
Thanks in advance.