Additionally, after seeing the new entries on the FAQ page, I noticed there are two different messages listed under Dataset File Status:
File read: OK.
or
VALID MD5
When using a dataset only of File read: OKs, I have been getting errors, but not with those that contain only a few File read: OKs and primarily VALID MD5s. Is there really a functional difference? Where does it lie between useful data and corrupted data?
When testing File read OK .d directories with Elgorithm's Chaos MD5 program, I could not select individual .d directories. When I manually zipped them using "Send To Compressed Folder" from right click options on Windows 7, the zipped file's MD5 Sum was not the same as the zip file on your servers. I am still guessing that the files weren't properly uploaded, but should they match if everything worked properly during the upload?
This error presents across Linux and Mac machines, both viewing through Firefox and a Windows 7 machine viewing through Iron (De-Google'd Chrome).
Firstly, when uploading relatively large file sets (over 14 files per set), the Data Set Viewing interface does not show all files within the set in its list-view format. Additionally, the number of files displayed is cut off at 14. I have not ran many tests on this error due to the time and data it would require to experiment with.
The particular data set I encountered this error with contains 19 files, and when using the Create Job page's "Select Stored Dataset" dialogue, the file count listed beside this data set is indeed 19. When viewed under Stored Datasets, the count is 14, and only 14 files are visible.
Secondly, the Storage Space Percentage reports between the Create Job and File Upload dialogue seems to disagree with the pie chart presented under the Accounts page. My account claims to have 11% of its total storage space available under the Account page, yet the Create Job page states that 96.2%.
Thank you for the suggestion. I have gotten the statistical data that the biochemist was looking for. Now they want to run a 9 by 9 comparison, which will exceed the XCMSOnline data size limit per account by quite a significant margin. So I have to find a way to get the same results from the XCMS R package. Does the offline program produce a Diffreport in the same format as the online version?
I assume it does not handle .d Directories. Should we expect the same results with a .d directory as with an .mzdata.xml file?
We have successfully started generating statistical data, but it violated our understanding of the columns.
Our entry in question had a fold change of 2,434.4, but had a p value of 0.499, which is statistically insignificant. What is the test that is being used? We expected that a high fold change would indicate statistically significant differences between two sets of data. These tests were run using the "into" test.
Thank you. Some of the labels still seem ambiguous though.
If I sort by Retention Time and look at the p-value, this should tell me the statistical significance of the difference between the peaks in the control group and the experimental group. If this is correct we are, as they say, in business.
Let me preface my questions by stating the various violations for my specific case.
1) - I am not a chemist or biochemist. I am computer scientist working for a biochemist attempting to determine whether or not this tool will meet the needs of my employer for the purposes of our limited statistical tests. 2) - Our project is dealing with Mass Spectrometry of Lipids, not Proteins. Much of the software I have found is specifically geared towards dealing with Proteins, but this tool may be more general.
While attempting to figure out what relation each column in the output of a comparison of two mzData files produced by MassHunter, compared using the HPLC/Q-TOF protocol, we determined we did not have a good understanding of what each of these columns meant:
Feature - Assumed to mean the order in which a particular m/z value was discovered. Not clear that this is or isn't the case though.
Fold Change - This appears to be more or less the result of Control / Experiment x? columns. What those mean and by extension what this means is unclear
m/z - I am aware that this is the mass/charge ratio, the quantity has very high precision, far more than can be accurate. At what point does it cut off the precision if at all? Does it ignore differences after a certain point?
Retention Time - Is this the actual Retention Time or the Corrected Retention Time? If it is corrected, what is the procedure it is using?
MaxInt - The label for this column is ambiguous, "Absolute Maximum Intensity for all Features in this row". I assume this means it is the the highest positive or negative intensity value, but what is a Row in this context?
dataset(x?) - The label for this column is ambiguous, "Mean Feature intensities for dataset #". Once again, the meaning of feature in context comes up.
Any help in nailing down what these terms mean would be much appreciated. I am fairly certain this software can meet our needs, which are, given a specific retention time, for a specific m/z intensity peak, find the m/z intensity peak that matches it in another data set and compare them to determine of they are statistically significant.
