Wiki¶

#Blackburn lipid biomarkers of active TB analysis overview

Brief description of the data from Suereta¶

We analyzed extracted lipids form intact aluminum foil disks using chloroform methanol. Samples were collected by different filter sizes; i.e. 01, 2.5 and 10 micrometer in size. You will notice in the excel sheet 'labeled separated_filters' there are samples with more than one entries (_10, _2.5, _01) which refer to the different filter sizes and for some filters there are more than one file. There is also another sheet labeled combined_filters which combined all the separate filters for a single sample.
The extracts mixed with 2,5-Dihydroxybenzoic acid and were analyzed using the MALDI Mass spectrometer.

The raw data were analyzed using an in-house developed pipeline, in combination with mycobacterial database, to identify M. tuberculosis lipids. In a separate search we used Metabosearch to identify human lipids.

Further Zandi, used the R package Mass Spectrometry Wavelet on both the separate and combined datasets. I will be attaching the data set from this analysis to the email.

In the sample list you will notice batch 1 (controls: E_127 to E_168; cases: TDRS_006 to TDRS_024) and batch 2 (TDRS_027 to TDRS_083). These were analyzed on two separate occasions on the MALDI-MS. We can see a batch effect when we look at the data after our analysis.

Important observations (Katie)¶

Strong technical artifacts in the dataset that are apparently also present within batch 1 between cases and controls, based on heavy autocorrelation detected in the dataset that currently precludes detection of robust biomarkers.
See plots under the files section for more.