Cannot download normalised data

[joshb]

In previous versions of MetaboAnalyst, you could download a .csv file of the normalised data, but it seems like this is no longer the case?

As an example, I am using the ‘NMR spectral bins’ test dataset (Psihogios NG, et al.). Using the ‘Show R commands’ option I am doing the following:

1.	mSet<-InitDataObjects(“specbin”, “stat”, FALSE)
2.	mSet<-Read.TextData(mSet, “Replacing_with_your_file_path”, “rowu”, “disc”);
3.	mSet<-SanityCheckData(mSet)
4.	mSet<-ReplaceMin(mSet);
5.	mSet<-SanityCheckData(mSet)
6.	mSet<-FilterVariable(mSet, “F”, 25, “none”, -1, “mean”, 0)
7.	mSet<-PreparePrenormData(mSet)
8.	mSet<-Normalization(mSet, “SamplePQN”, “NULL”, “ParetoNorm”, “C002”, ratio=FALSE, ratioNum=20)
9.	mSet<-PlotNormSummary(mSet, “norm_0_”, “png”, 72, width=NA)
10.	mSet<-PlotSampleNormSummary(mSet, “snorm_0_”, “png”, 72, width=NA)
11.	mSet<-PCA.Anal(mSet)
12.	mSet<-PlotPCAPairSummary(mSet, “pca_pair_0_”, “png”, 72, width=NA, 5)
13.	mSet<-PlotPCAScree(mSet, “pca_scree_0_”, “png”, 72, width=NA, 5)
14.	mSet<-PlotPCA2DScore(mSet, “pca_score2d_0_”, “png”, 72, width=NA, 1,2,0.95,0,0, “na”)
15.	mSet<-PlotPCALoading(mSet, “pca_loading_0_”, “png”, 72, width=NA, 1,2);
16.	mSet<-PlotPCABiplot(mSet, “pca_biplot_0_”, “png”, 72, width=NA, 1,2,10)
17.	mSet<-PlotPCA3DLoading(mSet, “pca_loading3d_0_”, “json”, 1,2,3)
18.	mSet<-SaveTransformedData(mSet)

If I then go to the ‘Download’ tab on left, I used to be able to download the .csv file of the normalised data. However, this option is not there anymore. Is it still possible to download the normalised datafile from MetaboAnalyst online? Thank you very much for the assistance.

[jeff.xia]

I don’t know what option you refer to. The normalized data is always shown as “data_normalized.csv” in the download page.

[joshb]

Thank you for your prompt reply! Unfortunately this is not showing for me - after doing all the above commands, here is what my download page options are (see screenshot). There is no data_normalized, and this is not in the zip folder either. Has this option disappeared?

[jeff.xia]

This is inexplicable to me, as I can see all those files following the steps. Maybe clear cache, close browser and try again. Do not open MetaboAnalyst using multiple tabs

[joshb]

I have now tried this on two different browsers and on two separate computers, clearing cookies/cache each time (and with three different datasets - two of the supplied test datasets and one of my own). In all cases, while I can see all the files that are shown in my screenshot, a “data_normalized.csv” file or similar is not there. I believe user ‘ggplum’ had the same issue in their post of May 20th but their post did not follow complete guidelines and so did not receive a reply. If you are able to send a screenshot of your downloads page with the normalized data file to confirm that it is still working for you, I will be happy to keep investigating independently why it is not working for me. Thank you for your continued assistance!

[GordonLI]

Thanks for confirming your steps. I’ve looked at the situation and performed the analysis myself, it looks like a few key files: data_processed.csv, data_original.csv, and data_normalized.csv aren’t appearing for you.

I noticed your browser might not be fully updated (there’s a “Relaunch to Update” prompt in the upper right corner). Please update your browser to the latest version and then try the analysis again. This could resolve compatibility issues.

Another quick way to check if it’s a browser issue is to open an Incognito window (press Ctrl + Shift + N in Chrome) and perform the analysis there. Incognito mode ignores your browser’s saved cache and settings. If the files appear in Incognito, it tells us the problem is likely with your regular browser’s cache or settings.

[Cqlzr_C]

我也遇到了同样的问题，下载不了normalized data，后来我发现把VPN关掉之后就有了

[joshb]

Thank you all for your helpful replies! I have tried updating my browser, going into incognito mode etc and those particular files still aren’t showing up for me (have now tried on three separate computers with two different OS!). However, it seems like given others can successfully download these files, it’s not a problem with MetaboAnalyst, rather with something on my end. I will keep troubleshooting; thanks for your efforts!