APOGEE Caveats

This page relays a list of known issues in the APOGEE data release.


We have separated these into two categories: (i) problems and bugs and (ii) fundamental limitations from either data or methodology. The former are known issues in the catalogs themselves (many discovered after the release), whereas the latter is more fundamental to what we can provide.

For additional discussion of certain issues, see the pages on Using APOGEE spectra, Using ASPCAP stellar parameters, and Using APOGEE stellar abundances.

Methodology and Data Limitations

Incorrect LSF for some LCO stars

For the initial ASPCAP run using the synspec grid, a bookkeeping error was made such that some of the LCO stars were processed using a non-optimal LSF grid, as it used the APO fiber LSF assignments rather than the LCO fiber assignments. This leads to small, but not negligible, changes in derived stellar parameters and chemical abundances for about 113,000 stars from LCO.

The affected LCO data have been reprocessed using the correct assignments and a corrected version of the files are found in the Science Archive Server under the synspec_rev1 directory tree; the revised summary file is allStar-dr17-synspec_rev1.fits

We recommend users adopt the synspec_rev1 results, but note that there will be inconsistencies with the subset of Value Added Catalogs that adopted stellar parameters and/or chemical abundances from the initial synspec run, which are found in the synspec file directory.

Lingering effects of LSF

Although ASPCAP currently attempts to account for LSF variations by splitting the analysis into groups by mean fiber number, there are indications that the mean and scatter in abundances of stars varies at a low level with the mean fiber number (few hundredths of a dex).

Erroneous extinctions for bright stars

For very bright objects, the WISE photometry employed to generate some extinction estimates can have significant problems, which leads to estimated extinctions that may be appreciably in error. This concern particularly impacts the bright star sample observed with the NMSU 1-meter.

Users are cautioned against using the tabulated extinctions for very bright stars.

Persistent effects of persistence

While the improved treatment of persistence seems to result in significantly better performance in the derivation of stellar parameters and abundances for stars affected by persistence, there are still some stars for which persistence likely leads to issues.

Users of the APOGEE spectra should pay careful attention to the persistence flags and should consider the use of the inflated uncertainties for persistence-affected pixels.

Atypical Abundance Ratios

Because ASPCAP works by varying element families together, inaccuracies can occur if aberrant/non-standard element abundance ratios are present in stars. For example, the ASPCAP parameter derivation is somewhat flawed in second-generation globular cluster stars, where non-standard oxygen abundances lead to systematic offsets in effective temperature and gravity, which in turn result in offsets in other quantities. Jönsson et al. (2020) provides a detailed discussion.

The Abundance Scale

The abundance scale, i.e., which solar abundances are used in the normalization of the supplied abundance ratios, is difficult to detangle, but we are likely to be close to the scale of Grevesse et al. (2007) for many elements. A complete description of the APOGEE abundance scale is provided on the ASPCAP page and Jönsson et al. (2020) provides a detailed discussion.


For stars in which all of the visit spectra were recorded in regions affected by persistence, the uncertainties for the pixels/wavelengths affected by persistence are significantly inflated. This detector-based problem has the effect of down-weighting pixels/wavelengths relative to those pixels/wavelengths that are not affected by persistence in the ASPCAP fits. Because the S/N that characterizes the combined spectra is the median S/N of all of the pixels, the standard S/N reported for these stars is reduced. To provide a better S/N estimate, we have also calculated an alternate S/N, SNREV, that is determined over a wavelength region in the middle chip that should not have many pixels that can be affected by persistence.

SNREV is the recommended quantity to use for S/N assessment.

Abundance Nodes

A subset of red giant stars with $T_{eff} \lt 4000 K$ exhibit “noding” in the abundances of a few elements. For reasons not yet fully understood ASPCAP prefers discrete abundance values for this subset of stars, resulting in tight sequences in the $[X/Fe]-[Fe/H]$ planes that we believe to be unphysical. The elements most affected by this “noding” are aluminum and chromium, with oxygen and calcium also showing this behavior for stars with supersolar metallicity. Users should be cautious when using the abundances of these elements for red giant stars with $T_{eff} \lt 4000 K$.

Rotation in Giants

Rotation is only included as a fitted parameter for the dwarf grids. For this reason, giant stars that are rotating may have suspect stellar parameters due to the spectral fits trying to compensate for the broadened lines.

Problems and Bugs

VHELIO is in Barycentric Frame

In the allVisit and allStar files, the VHELIO entry is in the barycentric frame, not the heliocentric frame as the name suggests. The naming convention has been maintained from earlier releases for historical reasons. The data model has been corrected to more clearly convey this information to the user.

Incorrect telescope values in some LCO FITS headers

The asVisit and asPlate FITS files incorrectly have a header card TELESCOP='apo25m', when they should all have TELESCOP='lco25m'. These files can all easily be identified as being derived from LCO observations by their filename prefixes (as) and by their location in the directory tree.

Inconsistent Population of Named Tags

Stars with the M_H_BAD flag set should have their named tag abundances unpopulated, however there are some stars who have this flag set and some populated named abundance tags.

We advise those using named tag abundances to check if the M_H_BAD flag is set, and if it is set to treat such abundances with caution.

Targeting Caveats

This section contains items unique to APOGEE-2 processing. Caveats and issues with APOGEE-1 observations are documented here.

Multiple target classes

Some targets may have been selected independently for distinct science programs within different visits to the same field. When we combine spectra, the target flag that we adopt for the combined spectrum is a bitwise OR of all of the target flags of the individual visit spectra. As a result, there are stellar spectra constructed from multiple visits for which a target flag bit may be set in the combined spectra, but not in all of the visit spectra that were used to construct it.

APOGEE-2S Field-of-View

APOGEE-2S plates have a full field-of-view with a radius of $0.95^{\circ}$. However, most of the APOGEE-2S plates were designed to have a reduced field-of-view of only $0.80^{\circ}$. This choice occurred due to the vignetting along the edges of the du Pont telescope (APOGEE-2S) field-of-view.

Users modeling the selection function for APOGEE-S data are encouraged to check the field-of-view for the plates used in their analysis.

Duplicate Targets

For certain fields which overlap one another, a few stars were inadvertently targeted in both fields. Since spectra are combined only within a field, these stars appear more than once in the combined spectra and summary files/tables. When multiple combined spectra of the same object exist, the lower S/N observations all have a bit set in the EXTRATARG bitmask that appears in the summary allStar file and in the CAS table.

The EXTRATARG bit should allow users to avoid the duplicate use of the same target in an analysis.

Inconsistent IDs

For objects observed with the NMSU 1-meter (TELESCOPE of "apo1m"), alternate object names were used for observation and reduction. 2MASS identifications, however, have been adopted in the final summary files and associated database tables. If users want to find the individual star spectrum files (e.g., the apStar or aspcapStar files), they will need to know the star name used during the reduction, which is stored in the ALT_ID tag.

Users should check the ALT_ID tag before seeking individual spectrum files for NMSU 1-meter observations.

Targeting Flag for 1-meter data

For objects observed with the NMSU 1-meter (telescope = apo1m), APOGEE2_TARGET2 bit 22 was not set. The 1-meter data can still be isolated using the telescope tag.

Users should identify 1-meter data using telescope = 'apo1m' instead of using APOGEE2_TARGET2.