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Messages - trammells

1
XCMS Online / Re: Problem uploading files
Hi, I see what you mean now. There does not appear to be an error with changing settings. I just didn't follow the directions. My apologies.
2
XCMS Online / Re: Problem uploading files
Hi, I think you misunderstood. I couldn't change the parameters before I began the job. I had uploaded the dataset. I had gone to change the parameters before submitting the job. I was not able to in either internet explorer, firefox, or chrome.
3
XCMS Online / Re: Problem uploading files
Hi, thank you for your prompt reply.

 I have tried uploading to the dataset uploading area as well without much luck. However, I was able to upload data using internet explorer in both the stored data tab and in the create job area. Another problem arose though in all three browsers that I tried (chrome, firefox, and internet explorer) where I could not change job parameter settings. They were all grayed out.
4
XCMS Online / Problem uploading files
I am having problems uploading files for analysis. I converted the Waters .raw files to .cdf. I had uploading other files from the same run converted today and analyzed them no problem. However, my attempts to upload other files have failed. The upload window loads, I am able to name the data set as well. The files come up in the directory and appear to load to the window, however, upon loading, the window does not close and the files are 'uploading' continuously according to the stored data tab. I have tried with both chrome and firefox. Firefox will not even allow me to upload files, though the upload window does load. I am running on Toshiba satellite laptop with windows 7 operating system.
5
XCMS / Re: Heat Map Visualization
Thank you very much for the reply. I am on my way to making a better figure. However, I am wondering how I can group the files such that the control conditions files are merged to one dataset and the treatment is another. I want to display differences between the control condition and the treatment.
6
XCMS / Heat Map Visualization
Hi,

 I have been attempting to visualize the data as a heat map but haven't found much luck in doing so. Ideally, I'd love to display the data showing changes in abundance with color between two conditions compared to a control group. Does anyone know the correct R code to perform this action? I have looked for the code to make a heat map but I really need something more similar to how microarray data is displayed.

Thank you for your input and if you require further information, please do not hesitate to ask,

Sam
7
XCMS Online / Analytical versus Biological Replicates
Hello,

 I have a statistical question. I have three biological replicates and for each biological replicates two injections (2 analytical replicates). When performing an analysis, I see no way to differentiate between the two types of data sets. I have concerns that with an n of 6 compared to 3, some intensities may be made more significant than they are. However, I clearly want to control for machine produced error. Does anyone have any suggestions for dealing with this problem?

Thank you,

Trammells